Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Bayes Theorem: A theorem in probability theory named for Thomas Bayes (1702-1761). In epidemiology, it is used to obtain the probability of disease in a group of people with some characteristic on the basis of the overall rate of that disease and of the likelihood of that characteristic in healthy and diseased individuals. The most familiar application is in clinical decision analysis where it is used for estimating the probability of a particular diagnosis given the appearance of some symptoms or test result.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Likelihood Functions: Functions constructed from a statistical model and a set of observed data which give the probability of that data for various values of the unknown model parameters. Those parameter values that maximize the probability are the maximum likelihood estimates of the parameters.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Fossils: Remains, impressions, or traces of animals or plants of past geological times which have been preserved in the earth's crust.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Markov Chains: A stochastic process such that the conditional probability distribution for a state at any future instant, given the present state, is unaffected by any additional knowledge of the past history of the system.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Genetic Variation: Genotypic differences observed among individuals in a population.Monte Carlo Method: In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Computer Simulation: Computer-based representation of physical systems and phenomena such as chemical processes.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Classification: The systematic arrangement of entities in any field into categories classes based on common characteristics such as properties, morphology, subject matter, etc.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.RNA, Ribosomal, 28S: Constituent of the 60S subunit of eukaryotic ribosomes. 28S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Phylogeography: A field of study concerned with the principles and processes governing the geographic distributions of genealogical lineages, especially those within and among closely related species. (Avise, J.C., Phylogeography: The History and Formation of Species. Harvard University Press, 2000)Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.Genetics, Population: The discipline studying genetic composition of populations and effects of factors such as GENETIC SELECTION, population size, MUTATION, migration, and GENETIC DRIFT on the frequencies of various GENOTYPES and PHENOTYPES using a variety of GENETIC TECHNIQUES.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Metagenomics: The genomic analysis of assemblages of organisms.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Exome: That part of the genome that corresponds to the complete complement of EXONS of an organism or cell.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.INDEL Mutation: A mutation named with the blend of insertion and deletion. It refers to a length difference between two ALLELES where it is unknowable if the difference was originally caused by a SEQUENCE INSERTION or by a SEQUENCE DELETION. If the number of nucleotides in the insertion/deletion is not divisible by three, and it occurs in a protein coding region, it is also a FRAMESHIFT MUTATION.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Genetic Speciation: The splitting of an ancestral species into daughter species that coexist in time (King, Dictionary of Genetics, 6th ed). Causal factors may include geographic isolation, HABITAT geometry, migration, REPRODUCTIVE ISOLATION, random GENETIC DRIFT and MUTATION.Human Genome Project: A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.Genes, Bacterial: The functional hereditary units of BACTERIA.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Haplotypes: The genetic constitution of individuals with respect to one member of a pair of allelic genes, or sets of genes that are closely linked and tend to be inherited together such as those of the MAJOR HISTOCOMPATIBILITY COMPLEX.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.Information Storage and Retrieval: Organized activities related to the storage, location, search, and retrieval of information.Database Management Systems: Software designed to store, manipulate, manage, and control data for specific uses.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Geography: The science dealing with the earth and its life, especially the description of land, sea, and air and the distribution of plant and animal life, including humanity and human industries with reference to the mutual relations of these elements. (From Webster, 3d ed)Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.DNA, Chloroplast: Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Genes, Mitochondrial: Genes that are located on the MITOCHONDRIAL DNA. Mitochondrial inheritance is often referred to as maternal inheritance but should be differentiated from maternal inheritance that is transmitted chromosomally.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Data Compression: Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.Ascomycota: A phylum of fungi which have cross-walls or septa in the mycelium. The perfect state is characterized by the formation of a saclike cell (ascus) containing ascospores. Most pathogenic fungi with a known perfect state belong to this phylum.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Selection, Genetic: Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.Databases, Protein: Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.ComputersAngiosperms: Members of the group of vascular plants which bear flowers. They are differentiated from GYMNOSPERMS by their production of seeds within a closed chamber (OVARY, PLANT). The Angiosperms division is composed of two classes, the monocotyledons (Liliopsida) and dicotyledons (Magnoliopsida). Angiosperms represent approximately 80% of all known living plants.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Plastids: Self-replicating cytoplasmic organelles of plant and algal cells that contain pigments and may synthesize and accumulate various substances. PLASTID GENOMES are used in phylogenetic studies.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.Genes, Plant: The functional hereditary units of PLANTS.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Gene Flow: The change in gene frequency in a population due to migration of gametes or individuals (ANIMAL MIGRATION) across population barriers. In contrast, in GENETIC DRIFT the cause of gene frequency changes are not a result of population or gamete movement.Bacterial Proteins: Proteins found in any species of bacterium.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.South AmericaPlants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Metagenome: A collective genome representative of the many organisms, primarily microorganisms, existing in a community.Computer Graphics: The process of pictorial communication, between human and computers, in which the computer input and output have the form of charts, drawings, or other appropriate pictorial representation.Acari: A large, subclass of arachnids comprising the MITES and TICKS, including parasites of plants, animals, and humans, as well as several important disease vectors.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Mycological Typing Techniques: Procedures for identifying types and strains of fungi.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Models, Statistical: Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.DNA Barcoding, Taxonomic: Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".Gene Order: The sequential location of genes on a chromosome.Information Systems: Integrated set of files, procedures, and equipment for the storage, manipulation, and retrieval of information.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.Biodiversity: The variety of all native living organisms and their various forms and interrelationships.CD-ROM: An optical disk storage system for computers on which data can be read or from which data can be retrieved but not entered or modified. A CD-ROM unit is almost identical to the compact disk playback device for home use.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Lemur: A genus of the family Lemuridae consisting of five species: L. catta (ring-tailed lemur), L. fulvus, L. macaco (acoumba or black lemur), L. mongoz (mongoose lemur), and L. variegatus (white lemur). Most members of this genus occur in forested areas on Madagascar and the Comoro Islands.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Sequence Tagged Sites: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Genome, Chloroplast: The genetic complement of CHLOROPLASTS as represented in their DNA.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.Basidiomycota: A phylum of fungi that produce their sexual spores (basidiospores) on the outside of the basidium. It includes forms commonly known as mushrooms, boletes, puffballs, earthstars, stinkhorns, bird's-nest fungi, jelly fungi, bracket or shelf fungi, and rust and smut fungi.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.North AmericaFruiting Bodies, Fungal: The fruiting 'heads' or 'caps' of FUNGI, which as a food item are familiarly known as MUSHROOMS, that contain the FUNGAL SPORES.Mutation Rate: The number of mutations that occur in a specific sequence, GENE, or GENOME over a specified period of time such as years, CELL DIVISIONS, or generations.Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.

*  Personal genomics and rat poison - Discovering Biology in a Digital World
Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern… ... I also think all the data is in adults. There's no relaible data on using the genotype information in pediatrics. ... Molecular Biology Genome Genomics HIV/AIDS Holidays Humor Microbiology Miscellany Mitochondria MMDB molecular structures ... PubMed Reviews Science Art Science careers Science culture Science education science outreach Seattle Second Life sequence ...
http://scienceblogs.com/digitalbio/2009/05/05/personal-genomics-and-rat-pois/
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Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern… ... Molecular Biology Genome Genomics HIV/AIDS Holidays Humor Microbiology Miscellany Mitochondria MMDB molecular structures ... PubMed Reviews Science Art Science careers Science culture Science education science outreach Seattle Second Life sequence ...
http://scienceblogs.com/digitalbio/tag/fremont-fair/
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Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern… ... Molecular Biology Genome Genomics HIV/AIDS Holidays Humor Microbiology Miscellany Mitochondria MMDB molecular structures ... PubMed Reviews Science Art Science careers Science culture Science education science outreach Seattle Second Life sequence ... ... AIDs doctors held prisoner by Iran Discovering Biology in a Digital World. Science Blogs Go to. Joan Bushwell s Chimpanzee Refuge Effect Measure Eruptions evolgen Evolution for Everyone Evolving Thoughts Framing Science Galactic Interactions Gene Expression Genetic Future Good Math, Bad Math Green Gabbro Guilty Planet Integrity of Science Intel ISEF Laelaps Life at the SETI Institute Live from ESOF 2014 Living the Scientific Life Scientist, Interrupted Mike the Mad Biologist Mixing Memory Molecule of the Day Myrmecos Neuron Culture Neurontic Neurophilosophy Neurotopia Not Exactly ...
http://scienceblogs.com/digitalbio/2009/01/08/aids-doctors-held-prisoner-by/
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Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern… ... Molecular Biology Genome Genomics HIV/AIDS Holidays Humor Microbiology Miscellany Mitochondria MMDB molecular structures ... Sequencing the campus at the Johns Hopkins University. Posted by Sandra Porter of Digital World Biology on July 24, 2006 ... We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the
http://scienceblogs.com/digitalbio/tag/16s-rrna/
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Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern… ... Molecular Biology Genome Genomics HIV/AIDS Holidays Humor Microbiology Miscellany Mitochondria MMDB molecular structures ... PubMed Reviews Science Art Science careers Science culture Science education science outreach Seattle Second Life sequence ...
http://scienceblogs.com/digitalbio/2008/08/15/vaccines-part-ii-what-are-vacc/
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... sequences among modern human groups ...
http://godandscience.org/evolution/sld023.html
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Using available genomic sequence data on coagulation factor VIII and predictive models of molecular evolution, we engineer ... Based on the enhanced in vitro biosynthesis data obtained for An-53, and on its higher degree of sequence similarity to hFVIII ... Ancestral sequences were inferred using both DNA and amino acid-based models in PAML VERSION 4.1 29. The multiple sequence ... 1). Available extant sequence data was sufficient to accurately extend the phylogenetic tree and infer ancestral (An)-FVIII
http://pubmedcentralcanada.ca/pmcc/articles/PMC5225049/
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Such evidence may come from pattern (DNA sequence comparisons or the fossil record)." (Icons, p. 66) So have molecular data ... through the use of molecular data, for example), again avoiding circularity." (Denying Evolution, p. 254) But Wells anticipates ... When Pigliucci disagrees with Wells, he repeatedly puts words in in the latter's mouth and cites evidence or data that doesn't ... Instead he states that, "Only a few misguided molecular biologists (ignorant of evolution)" have claimed that "There
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... preliminary molecular data support the existence of at least three other flagellar kinesins (Bernstein, 1995) increasing the ... The pf16 gene product is a 57-kD protein with sequence similarity to armadillo repeat proteins (Smith and Lefebvre, 1996) whose ... Further biochemical and molecular characterization of the CPC1 gene product should expand our understanding of the mechanisms ... Our data extend previous antibody studies that identified several kinesin-like proteins in the central pair ...
http://jcb.rupress.org/content/144/2/293
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2007) analysed sequence data from two mtDNA (COI and 16S) and three nDNA (18S, 28S and histone H3) markers. Two independent ... Morphological and molecular data (Piano et al. 1997) recover two congruent clades. One clade originated on Kauai and via ... Although co-speciating lineages in the Hawaiian Islands are yet to be investigated using molecular data, they nevertheless hold ... 2003). However, recent molecular data confirm that the Hawaiian drosophilids (Drosophila and Scaptomyza) are monophyletic
http://rstb.royalsocietypublishing.org/content/363/1508/3363
*  CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S12/CH391L/S12/Ancestral Sequence Reconstruction From OpenWetWare CH391L/S12 Revision as of 15:45, 13 February 2012 by Jared Ellefson Talk. 1 What is Ancestral Sequence Reconstruction. 1.1 Pipeline for Generating Ancestral Genes 1.1.1 Methods of Inferring Ancient Sequences 1.1.2 Gene Synthesis 1.1.3 Testing Ancestral Variants. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral Pigments 1.2.2 Inferring the Paleoenvironment of ancient Earth. What is Ancestral Sequence Reconstruction. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. Sequence Reconstruction Example. Sequences from extant species of the desired common ancestral gene and outgroup genes are aligned. The ancestral gene is inferred based on evolutionary models typically maximum parsimony or maximum likelihood. Ancestral genes ...
http://openwetware.org/index.php?title=CH391L/S12/CH391L/S12/Ancestral_Sequence_Reconstruction&oldid=583945
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was ...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=677463&oldid=677462
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... CH391L/S13/Ancestral Sequence Reconstruction From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 19:53, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments ← Previous diff. Revision as of 19:55, 24 February 2013 view source Aurko Dasgupta Talk. contribs → Evolution of Coral Pigments Next diff →. Line 30:. Line 30:. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red cite #Ugalde /cite. The details of the evolution of fluorescent color in the GFP superfamily was not fully understand. That is, what fluorescent spectra did the common ancestors of the modern corals have. One example of ancestral sequence reconstruction was done by the Matz group currently residing at the University of Texas at Austin. Fluorescent proteins from related ...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678933&oldid=678932
*  Branching order of bacterial phyla (Gupta, 2001)
branching order of bacterial phyla gupta branching order of bacterial phyla gupta bacterial phyla there are several models of the branching order of bacterial phyla one of these was proposed in by gupta based on conserved indels or protein termed protein signatures an alternative approach to molecular phylogeny some problematic exceptions and conflicts are present to these conserved indels however they are in agreement with several groupings of classes and phyla one feature of the cladogram obtained with this method is the clustering of cell wall morphology with some exceptions from monoderms to transitional diderms to traditional diderms in the cladogram below yellow pseudopeptidoglycan monoderms gram variable red thick peptidoglycan monoderms gram positive blue thin peptidoglycan diderms gram negative green atypical see note in parethesis cladex style width auto bar gold archaea cladex bar crimson firmicutes cladex bar crimson actinobacteria see also branching order of bacterial phyla woese ...
https://en.wikipedia.org/wiki/Branching_order_of_bacterial_phyla_(Gupta,_2001)
*  CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. Fluorescent proteins from related coral species had wavelengths corresponding to Cyan, Green, and Red. That is, what fluorescent spectra did the common ancestors of the modern corals have. Sequences for the common ancestor nodes were synthesized and tested for their activity. The common ancestor to all the superfamily had a green emission peak. The more recent common ancestor of Green/Red had two emission peaks; a strong green peak and a smaller red peak. 1.2 Examples of Ancestral Sequence Reconstructions 1.2.1 Evolution of Coral ...
http://openwetware.org/index.php?title=CH391L/S13/Ancestral_Sequence_Reconstruction&diff=678913&oldid=678912
*  The FASTML Server - Server for computing Maximum Likelihood ancestral sequence reconstruction
the fastml server server for computing maximum likelihood ancestral sequence reconstruction home overview gallery source code citing credits old version the fastml server server for computing maximum likelihood ancestral sequence reconstruction type your multiple sequence alignment msa fasta format only or upload your multiple sequence alignment msa file sequences type amino acids nucleotides codons type your phylogenetic tree optional newick format only or upload phylogenetic tree file newick format only model of substitution jtt default lg mtrev for mitochondrial proteins cprev for chloroplasts proteins wag dayhoff jc model jukes and cantor t model tamura hky model hasegawa kishino and yano gtr generalised time reversible yang for codon sequences empiricodon for codon sequences please enter your email address optional your email address will be used to update you the moment the results are ready load an example advanced options phylogenetic tree method ...
http://fastml.tau.ac.il/
*  Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction
... Inquiry-based Integrated Instructional Units Comparison of Protein Sequences: BLAST searching and Phylogenetic Tree Construction. It accompanies several weeks of wet lab work in which students clone cDNAs encoding Cytochrome P450 1A CYP1A from animals primarily fish collected locally and exposed to pollution compounds that induce expression of the enzyme. In this exercise, students perform BLAST searches of reported CYP1A sequences and construct phylogenetic trees using CYP1A amino acid sequences from various vertebrate species, especially those with multiple CYP1A paralogs. Thus, evolutionary analysis of CYP1A sequences from many species provides an opportunity to explore the number and timing of gene duplications during vertebrate evolution. Three short readings about gene duplication in evolution and phylogenetic analysis are provided at least one week prior to class. These readings complement earlier readings that specifically concern the cloning and evolutionary analysis ...
http://serc.carleton.edu/genomics/units/19100.html
*  Talk:CH391L/S13/Ancestral Sequence Reconstruction - OpenWetWare
... Talk:CH391L/S13/Ancestral Sequence Reconstruction. From OpenWetWare. Talk:CH391L/S13 Revision as of 00:02, 24 February 2013 by Aurko Dasgupta Talk. contribs. diff ←Older revision. Current revision diff. Newer revision→ diff. Jump to: navigation, search. Gabriel Wu 16:59, 18 February 2013 EST : Remove the cost and methods of gene synthesis or just reference the dna assembly section we've already gone over. Expand the codon optimization section unless this fits better in somewhere else. Gabriel Wu 16:59, 18 February 2013 EST : How does Pauling's proposal for ancestral gene construction relate to the actual discovery of DNA structure. Benjamin Gilman 13:21, 21 February 2013 EST : The Pauling and Zuckerkandl paper came out when the only protein sequence information we had came from limited peptide sequencing methods like Edman degradation N-terminal sequencing. You might add something about the shift to using DNA or RNA sequences to infer protein sequence once techniques like ...
http://openwetware.org/index.php?title=Talk:CH391L/S13/Ancestral_Sequence_Reconstruction&direction=prev&oldid=678776
*  Ancestral reconstruction
'Ancestral Reconstruction' also known as 'Character Mapping' or 'Character Optimization' is a method in evolutionary biology by which one can attempt to understand the phenotypic and genetic states of organisms that lived millions of years ago. Maximum Parsimony. Maximum likelihood. They are: maximum parsimony, maximum likelihood, and the Bayesian Inference. Maximum parsimony is the method that came about first. Maximum likelihood accounts for what we know about the likelihood of various events, which is that they are not all equal. Maximum Parsimony. Maximum Parsimony. Maximum likelihood. The main difference between this and maximum parsimony is that the maximum likelihood test accounts for the fact that not all events are equally likely to happen. When this is the case, maximum parsimony may actually be more accurate because it is more willing to make large, unlikely leaps than maximum likelihood is. Maximum likelihood has been shown to be quite reliable in reconstructing character states however it does ...
https://en.wikipedia.org/wiki/Ancestral_reconstruction
*  Viral phylodynamics
... Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread,. Methods Coalescent theory and phylodynamics. Examples Phylodynamics of Influenza. Phylodynamics of HIV. The clustering of taxa on a viral phylogeny will be affected by host population structure see figure 2 Viruses within similar hosts, such as hosts that reside in the same geographic region, are expected to be more closely related genetically if transmission occurs more commonly between them. For example, an application to HIV sequences within infected hosts showed that viral substitution rates dropped to effectively zero following the initiation of antiretroviral drug therapy. If the population size N t changes over time, the coalescent rate \lambda n t will also be a function of time. derived this rate for a time-varying population size under the ...
https://en.wikipedia.org/wiki/Viral_phylodynamics
*  Diagnostic characters from Consortium of mx users. - Encyclopedia of Life
... Diagnostic characters. 2011, by Lewis L. Deitz and Matthew S. Wallace. Add to a collection. Diagnostic characters. Distance from eye to base of forewing usually greater than half eye width exceptions: Deiroderes and many Nicomiinae. Pronotum usually produced posteriorly over scutellum exceptions: Endoiastinae, Nicomiinae, Deiroderes, Abelus, and Hemicentrus, often also with anterior, lateral, or dorsal projections. Forewings with vein M fused with Cu basally share common stem; exceptions: some Nicomia and some Smiliinae. Prothoracic trochanter and femur not fused. Male abdominal segment IX usually with lateral plates discrete from pygofer exceptions: fused to pygofer in few members of various tribes; lateral plates absent in Anchistrotus and some Stegaspidini. Female pygofer not strongly produced posteroventrally. Nymph with abdominal tergum IX forming sheath around segment X, anal opening dorsal or posterior. Latest updates. No one has provided updates yet. Learn how to contribute. Add a new comment. ...
http://eol.org/data_objects/12685167
*  Browse By Person: Phillips, Matthew | QUT ePrints
Browse By Person: Phillips, Matthew. Browse By Person: Phillips, Matthew Statistics dashboard. Review. Book Chapter Phillips, Matthew J. Penny, David 2010 Mammalian phylogeny., Phillips, Matthew J. PLoS ONE, 10 5, e0125723., Carrano, Matthew T. Systematic Biology. Phillips, Matthew J., Gibb, Gillian C. 2014 Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology and Evolution, 31 9, pp., Phillips, Matthew J. Phillips, Matthew J., Gibb, Gillian,. Bunce, Michael 2013 Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE, 8 2, pp. Phillips, Matthew J. Current Biology, 23 14, R603-R605., Phillips, Matthew J. Molecular Phylogenetics and Evolution, 59 3, pp., Phillips, Matthew J. 2010 Evolutionary relationships and divergence times among the native rats of Australia. 2009 The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. 2009 Accounting for calibration uncertainty in ...
http://eprints.qut.edu.au/view/person/Phillips,_Matthew.html
*  Wiegmann Lab: Current Research
Insect Molecular Systematics at NCSU. phylogenetic relationships and testing hypotheses about the evolution and diversification of insects. A major component of these studies is uncovering patterns and processes of DNA sequence evolution and using these to improve interpretation of morphological and developmental evolutionary pathways. Molecular Phylogenetics of Diptera: FLYTREE - NSF - Assembling the Tree of Life project on Diptera a Collaborative Research Effort in Dipteran Phylogenetics. The need for new, large, comprehensive datasets for Diptera phylogeny motivates our collaborative, National Science Foundation funded, Assembling the Tree of Life ATOL project-- FLYTREE. Within this study, we are assembling multiple phylogenetic data sets to simultaneously assess dipteran phylogenetic relationships and the information content of specific character systems. For example, we will compare large by character data sets 1st tier; 45 taxa; 15-20 genes and mt genomes to ...
http://www4.ncsu.edu/unity/users/b/bwiegman/public_html/labweb/currentresearch.html
*  Talk:CH391L/S13/DirectedProteinEvolution - OpenWetWare
Gabriel Wu Talk. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. *' ] 21:45, 21 February 2013 EST ':It would be nice if you added literature examples of Directed Evolution of Proteins for each approach as done in the Ancestral Sequence Reconstruction or take a similar approach. + *' ] 15:33, 2 March 2013 EST ':It would be nice to put some numbers on the typical plasmid screening in 'E. + ****' ] 14:03, 4 March 2013 EST ': This is an interesting point. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. *' ] 04:13, 27 February 2013 EST ':I thought it'd be nice to have a section explaining fitness landscapes and moving through sequence space. It's true that many times the selection will result in being trapped in a local optima, but ...
http://openwetware.org/index.php?title=Talk:CH391L/S13/DirectedProteinEvolution&diff=680636&oldid=680003
*  Systematics
thumb|400px|A comparison of phylogenetic and phenetic concepts Biological '''systematics''' is the study of the diversification of living forms, both past and present, and the relationships among living things through time. Phylogenetic trees of species and higher taxa are used to study the evolution of traits e.g., anatomical or molecular characteristics and the distribution of organisms biogeography. Systematics, in other words, is used to understand the evolutionary history of life on Earth. Definition and relation with taxonomy Taxonomic characters See also References Notes. Definition and relation with taxonomy. Europeans tend to use the terms "systematics" and "biosystematics" for the field of the study of biodiversity as a whole, whereas North Americans tend to use "taxonomy" more frequently. Taxonomic characters. Molecular characters. Immunological distance Electrophoretic differences Amino acid sequences of proteins DNA hybridization DNA and RNA sequences Restriction ...
https://en.wikipedia.org/wiki/Systematics
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Difference between revisions of "Molecular Systematics Spring 2014" From EEBedia. Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Lab%208.%20Kasey%20Pregler%20MiniPresentation%2012April12.pdf}}EEB 5350 Lab 8. Kasey Pregler MiniPresentation 12April12.pdf. Instructor: Chris Simon, Biopharm 305D, 6-4640, chris.simon@uconn.edu Graduate Assistant: Chris Owen, Biopharm 325A, christopher.l.owen@uconn.edu ; 6-3947. Readings: will be posted as PDF’s. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, among-site rate variation, taxon sampling, long branches, big trees, heterogeneous rates of evolution among branches, covarion shifts. Syllabus Molecular Systematics rev 28 Mar 12.pdf Assignment 1. ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21831&oldid=21782
*  Molecular phylogenetics
'Molecular phylogenetics ' is the branch of phylogeny that analyses hereditary molecular differences, mainly in DNA sequences, to gain information on an organism's evolutionary relationships. History of molecular phylogenetics Techniques and applications Theoretical background Limitations of molecular systematics See also Notes and references Further reading External links. A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly, multiple sequence alignment, model-test testing best-fitting substitution models and phylogeny reconstruction using Maximum Likelihood and Bayesian Inference, is available at Nature Protocol Bast, F. These have been replaced in recent times largely by DNA sequencing, which produces the exact sequences of nucleotides or 'bases' in either DNA or RNA segments extracted using different techniques. In a molecular systematic analysis, the haplotypes are ...
https://en.wikipedia.org/wiki/Molecular_phylogenetics
*  CH391L/S13/DNA Computing - OpenWetWare
... CH391L/S13/DNA Computing From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 11:55, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m New page: Hello world. ← Previous diff. Revision as of 12:03, 1 April 2013 view source Dwight Tyler Fields Talk. contribs m Next diff →. Line 1:. Line 1:. - Hello world. + ] ]. + =Introduction=. + Ancestral Sequence Reconstruction refers to the construction of hypothesized protein or DNA sequences belonging to a common ancestor of extant proteins or DNA. It enables scientists to synthesize biomolecules from extinct organisms. Sequence information Nucleic Acid and Protein from extant species can be used to infer the sequences of common ancestor species which can be synthesized and tested in the lab. The method was originally discussed by Pauling and Zuckerkandl in 1963 cite Pauling /cite, almost 30 years before the theory was experimentally tested. + ]. + + ==Pipeline for Generating Ancestral ...
http://openwetware.org/index.php?title=CH391L/S13/DNA_Computing&diff=687401&oldid=687389
*  Phylogenetic Classification ( Real World ) | Biology | CK-12 Foundation
Phylogenetic Classification Real World. Help. Help. You are viewing an older version of this Concept. Go to the latest version. Phylogenetic Classification. Practice Phylogenetic Classification Practice. 0% Practice Now. Evolution. Resources. Published. Cows Gone Wild. The "cows" you see are Aurochs Bos primigenius. They are the species of bovine that humans domesticated to form our modern day cows. Looking at the cave paintings of aurochs, you may get the sense that they were a bit different than our domesticated cattle. The characteristics which made aurochs successful in the wild were not the characteristics that humans thought were most useful. For example, packing on lots of meat may be a great trait in a cow for a cattle rancher, but if that meat hampers mobility, then it can make a cow an easy target to predators. This is one of the differences between artificial selection and natural selection. However, it does not take 600 years for noticeable changes to appear in bred species once the artificial ...
http://ck12.org/biology/Phylogenetic-Classification/rwa/21st-Century-Auroch/r8/
*  Filosofía, especie y sistemática
Host structure of the Phylogeny of West Nile Virus WNV: Does it shape the spatiotemporal structure. Methods Sequence Data: All the available sequences of complete genome of WNV, with collection times, and geographic locations 453 sequences, from 25 countries, and 79 hosts species were retrieved from GenBank. Phylogeny inferred using a Maximum likelihood analysis of 53 sequences. Phylogeny with Host structure for WNV. Just Testudines present a different resutl, where the non-nuclear and nuclear partitions had the lowest values Fig. Estimating Evolutionary Rates and Times to the last Common Ancestor DEV-2, using partitions vs complete coding region. Several studies have been aimed at understanding the epidemiology of DENV, rates and dates of evolution, and selection pressure in its different genes and genotypes Rico-hesse Rico-hesse, 1990; Rico-Hesse et al., 1997; S. The objectives of this study were to infer the time to the Most recent common ancestor MRCA of the DENV2 ...
http://elecsist.blogspot.com/
*  PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. | Broad Institute of MIT and
PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Broad Institute of MIT and Harvard. Partnerships Philanthropy Careers Contact Us. What is Broad. Our Approach Areas of Focus History Leadership Who is Broad Partner Institutions Artist-in-Residence Media Center. Press Room News from the Broad Photos for Journalists Spotlight: Ebola Spotlight: CRISPR BroadMinded Blog Video Library For the Scientific Community. Scientific Publications Science Data Software. Scientific Publications Science Data Software. Home. News & Publications:Scientific Publications PCA and clustering reveal alternate mtDNA phylogeny of N and M clades. Recent Broad Publications Inherited CHST11/MIR3922 deletion is associated with a novel recessive syndrome presenting with skeletal malformation and malignant lymphoproliferative disease. Read More / View Supplemental Materials Ferritinophagy via NCOA4 is required for erythropoiesis and is regulated by iron dependent HERC2-mediated proteolysis. Read More / ...
https://broadinstitute.org/publications/broad3822
*  Phylogenomics
It is a group of techniques within the larger fields of phylogenetics and genomics. Phylogenomics draws information by comparing entire genomes, or at least large portions of genomes. 1 Phylogenetics compares and analyzes the sequences of single genes, or a small number of genes, as well as many other types of data. Prediction of gene function Establishment and clarification of evolutionary relationships Gene family evolution Prediction and retracing lateral gene transfer. Prediction of Gene Function Prediction and Retracing Lateral Gene Transfer Gene family evolution Establishment of Evolutionary Relationships Databases See also References. Before the use of phylogenomic techniques, predicting gene function was done primarily by comparing the gene sequence with the sequences of genes with known functions. 3 This prediction was based on the fact that this organism has a gene for which the sequence is highly similar to genes from other species in the "MutS" gene ...
https://en.wikipedia.org/wiki/Phylogenomics
*  Wikiomics:RNA phylogenetics - OpenWetWare
... Wikiomics:RNA phylogenetics From OpenWetWare Difference between revisions Jump to: navigation, search Revision as of 17:04, 3 March 2008 view source Torsten Waldminghaus Talk. contribs added tags ← Previous diff. Current revision 05:34, 20 October 2009 view source Albert Vilella Talk. contribs adding rnasalsa. One intermediate revision not shown. Line 16:. Line 16:. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Bayesian Inference of Phylogeny. Allows secondary structure models. * Designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. Substitution models of sequence evolution that consider pairs of sites rather than single sites are implemented in this package along with standard nucleotides substitution models used nowadays. When a RNA molecule with a secondary structure is used in conjunction with a RNA substitution model, PHASE requires a structure-based alignment of the sequences with the ...
http://openwetware.org/index.php?title=Wikiomics:RNA_phylogenetics&diff=360520&oldid=189099
*  Polyphyly
Image:Monophyly, paraphyly, polyphyly.png File:Phylogenetic-Groups.svg|thumbnail|300px|Phylogenetic groups: A monophyletic taxon in yellow, the group of "reptiles and birds" contains a common ancestor and all of its descendants. A paraphyletic taxon in cyan, the reptiles contains its most recent common ancestor, but does not contain all the descendants of that ancestor. A polyphyletic in red, the group of all warm-blooded animals taxon does not contain the most recent common ancestor of all its members. A 'polyphyletic' Greek for "of many races" group is characterized by one or more homoplasies : phenotype s which have converged or reverted so as to appear to be the same but which have not been inherited from common ancestors. For example, warm-bloodedness evolved separately in the ancestors of mammals and the ancestors of birds 1. Researchers concerned more with ecology than with systematics may take polyphyletic groups as legitimate subject matter; the similarities in activity within the fungus group ' ...
https://en.wikipedia.org/wiki/Polyphyly
*  Difference between revisions of "Molecular Systematics Spring 2014" - EEBedia
Chris Simon. Chris Simon. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/EEB%205350%20Lab%209.%20Minipresentation%20RT-PCR%20Brigette.pdf}}EEB 5350 Lab 9. Minipresentation RT-PCR Brigette.pdf. Combining Data/Comparing Trees. + + :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Comparing%20Trees%20Combining%20Data%20Readings%202012.pdf}}Comparing Trees Combining Data Readings 2012.pdf. + + Reading for next week: :{{pdf|http://hydrodictyon.eeb.uconn.edu/courses/molsyst-eeb5350/Simon%2C%20Buckley%2C%20Frati%2C%20Stewart%2C%20Beckenbach%202006%20AREES%20%26%20supplement.pdf}}Simon, Buckley, Frati, Stewart, Beckenbach 2006 AREES supplement.pdf. Lectures will examine some of the most serious problems in evolutionary tree construction: nucleotide bias, alignment, homoplasy, ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Molecular_Systematics_Spring_2012&diff=21847&oldid=21846
*  Darwin's Evolutionary Tree 'Annihilated' | The Institute for Creation Research
Darwin s Evolutionary Tree Annihilated. Timely news related to creation and evolution. Life Sciences. Problems with Evolution. Evidence for Creation. Evidence for Truth. Evidence from Science. Apologetics Articles. ICR Store. Darwin's Evolutionary Tree 'Annihilated' by Brian Thomas, M.S. * Resources. Life Sciences Resources. Problems with Evolution. In 1837, Charles Darwin drew his first evolutionary tree in his B notebook, with the words I think scrawled above it, to illustrate his idea that all of today s species arose from a single common ancestor. But the poor fit of gene sequence data is forcing scientists to abandon the tree. A non-Darwinian evolutionary view has been offered, but this proposition is actually just the old Hopeful Monster with a twist. 3 Darwin s tree illustrated a long macroevolutionary past that never happened. 4 Finally, evolutionary biologists seem to be catching up with creation biologists. 5 Michael Syvanen, co-editor of Horizontal Gene Transfer 1998 and a medical ...
http://icr.org/articles/view/4404/295/
*  Phylogenetic profiling
... 'Phylogenetic profiling' is a bioinformatics technique in which the joint presence or joint absence of two traits across large numbers of species is used to infer a meaningful biological connection, such as involvement of two different proteins in the same biological pathway. Along with examination of conserved synteny, conserved operon structure, or "Rosetta Stone" domain fusions, comparing phylogenetic profiles is a designated a "post-homology" technique, in that the computation essential to this method begins after it is determined which proteins are homologous to which. A number of these techniques were developed by David Eisenberg and colleagues; phylogenetic profile comparison was introduced in 1999 by Pellegrini, 'et al.' Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. Method Theory Advances and Challenges Notes. For a given protein family, its presence or absence in each genome in the original formulation is represented by 1 present and 0 absent. The large number of complete ...
https://en.wikipedia.org/wiki/Phylogenetic_profiling
*  Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction
... - Wikibooks, open books for an open world. Structural Biochemistry/Analyzing protein structure and function using ancestral gene reconstruction. 1 Analyzing protein structure and function using ancestral gene reconstruction. Analyzing protein structure and function using ancestral gene reconstruction. Learning how protein sequence determines structure and function as well as learning the processes that generated the diverse structures and functions of extant proteins requires knowledge of the distribution of structures and functions through the multidimensional space of possible protein sequences. The outcomes of that massive experiment are preserved in the sequences, structures, and functions of modern-day protein families. Evolutionary analysis of these families can provide key insights into the nature of protein sequence space and the determinants of protein structure and function. Horizontal and Vertical Analysis. One way to study protein families is to identify candidate ...
https://en.wikibooks.org/wiki/Structural_Biochemistry/Analyzing_protein_structure_and_function_using_ancestral_gene_reconstruction
*  Patrocladogram
2 " and is used exclusively to determine the amount of divergence of a characteristic from a common ancestor. This means that cladistic and patristic distances are combined to construct a new tree using various phenetic algorithms. 3 The purpose of the patrocladogram in biological classification is to form a hypothesis about which evolutionary processes are actually involved before making a taxonomic decision. 4 Patrocladograms are based on biostatistics that include but are not limited to: parsimony, distance matrix, likelihood method s, and Bayesian probability. Some examples of genomically related data that can be used as inputs for these methods are: molecular sequences, whole genome sequences, gene frequencies, restriction site s, distance matrices, unique characters, mutations such as SNPs, and mitochondrial genome data. Cautions with patrocladogram usage Programs for patrocladogram analysis PATRISTIC. RAMI. Further reading References External links. Cautions with ...
https://en.wikipedia.org/wiki/Patrocladogram
*  SMART: DUF1866 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF1866
*  SMART: DUF3700 domain taxonomic distribution
smart duf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with duf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing duf domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DUF3700
*  SMART: PTPc motif domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PTPc motif domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PTPc motif domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PTPc_motif
*  SMART: HOX domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with HOX domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing HOX domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HOX
*  SMART: Citrate ly lig domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Citrate ly lig domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Citrate ly lig domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Citrate_ly_lig
*  SMART: Catalase domain taxonomic distribution
smart catalase domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with catalase domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing catalase domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Catalase
*  SMART: LRR RI domain taxonomic distribution
smart lrr ri domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with lrr ri domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing lrr ri domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LRR_RI
*  SMART: Fib alpha domain taxonomic distribution
smart fib alpha domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with fib alpha domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing fib alpha domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Fib_alpha
*  SMART: Frataxin Cyay domain taxonomic distribution
smart frataxin cyay domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with frataxin cyay domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing frataxin cyay domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Frataxin_Cyay
*  SMART: Integrin B tail domain taxonomic distribution
smart integrin b tail domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with integrin b tail domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing integrin b tail domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Integrin_B_tail
*  SMART: BMC domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with BMC domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing BMC domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=BMC
*  SMART: GA domain taxonomic distribution
smart ga domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ga domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ga domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GA
*  SMART: ELK domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ELK domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ELK domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ELK
*  SMART: SEC14 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with SEC14 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing SEC14 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SEC14
*  SMART: CP12 domain taxonomic distribution
smart cp domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cp domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cp domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CP12
*  SMART: NH domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with NH domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing NH domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NH
*  SMART: DM13 domain taxonomic distribution
smart dm domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dm domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dm domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DM13
*  SMART: LY domain taxonomic distribution
smart ly domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ly domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ly domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LY
*  SMART: zf-AD domain taxonomic distribution
smart zf ad domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with zf ad domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing zf ad domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=zf-AD
*  SMART: AWS domain taxonomic distribution
smart aws domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with aws domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing aws domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=AWS
*  SMART: Amelin domain taxonomic distribution
smart amelin domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with amelin domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing amelin domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Amelin
*  SMART: Ami 3 domain taxonomic distribution
smart ami domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with ami domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing ami domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Ami_3
*  SMART: C2 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with C2 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing C2 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=C2
*  SMART: CLH domain taxonomic distribution
smart clh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with clh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing clh domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CLH
*  SMART: CVNH domain taxonomic distribution
smart cvnh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with cvnh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing cvnh domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=CVNH
*  SMART: Cache 2 domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with Cache 2 domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing Cache 2 domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=Cache_2
*  SMART: ChSh domain taxonomic distribution
smart chsh domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with chsh domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing chsh domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ChSh
*  SMART: DAX domain taxonomic distribution
smart dax domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dax domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dax domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DAX
*  SMART: DEFSN domain taxonomic distribution
smart defsn domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with defsn domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing defsn domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DEFSN
*  SMART: DSHCT domain taxonomic distribution
smart dshct domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dshct domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dshct domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSHCT
*  SMART: DSPc domain taxonomic distribution
smart dspc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with dspc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing dspc domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=DSPc
*  SMART: EPEND domain taxonomic distribution
smart epend domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with epend domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing epend domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=EPEND
*  SMART: FBG domain taxonomic distribution
smart fbg domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with fbg domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing fbg domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=FBG
*  SMART: GPS domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with GPS domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing GPS domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GPS
*  SMART: GYR domain taxonomic distribution
smart gyr domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with gyr domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing gyr domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=GYR
*  SMART: HALZ domain taxonomic distribution
smart halz domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with halz domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing halz domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=HALZ
*  SMART: LNS2 domain taxonomic distribution
smart lns domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with lns domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing lns domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=LNS2
*  SMART: MltA domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with MltA domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing MltA domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MltA
*  SMART: MutL C domain taxonomic distribution
smart mutl c domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with mutl c domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing mutl c domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=MutL_C
*  SMART: NMU domain taxonomic distribution
smart nmu domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nmu domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nmu domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NMU
*  SMART: NRF domain taxonomic distribution
smart nrf domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nrf domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nrf domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NRF
*  SMART: NurA domain taxonomic distribution
smart nura domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with nura domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing nura domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=NurA
*  SMART: PA14 domain taxonomic distribution
smart pa domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with pa domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing pa domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PA14
*  SMART: PMEI domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with PMEI domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing PMEI domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=PMEI
*  SMART: ParB domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with ParB domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing ParB domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=ParB
*  SMART: RPEL domain taxonomic distribution
smart rpel domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with rpel domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing rpel domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RPEL
*  SMART: RasGAP domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with RasGAP domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing RasGAP domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=RasGAP
*  SMART: SPK domain taxonomic distribution
... SMART MODE: NORMAL GENOMIC. Schultz et al. 1998 Proc. Natl. Acad. Sci. USA 95, 5857-5864 Letunic et al. 2014 Nucleic Acids Res doi: 10.1093/nar/gku949 HOME. SETUP. FAQ. ABOUT. GLOSSARY. WHAT'S NEW. FEEDBACK. Taxonomic distribution of proteins with SPK domain. A species tree will be displayed here if you enable JavaScript in your browser. Click on the protein counts, or double click on taxonomic names to display all proteins containing SPK domain in the selected taxonomic class. 2014 EMBL Send comments to Ivica Letunic.
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SPK
*  SMART: SPRY domain taxonomic distribution
smart spry domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with spry domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing spry domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=SPRY
*  SMART: VRR NUC domain taxonomic distribution
smart vrr nuc domain taxonomic distribution smart mode normal genomic schultz et al proc natl acad sci usa letunic et al nucleic acids res doi nar gku home setup faq about glossary what s new feedback taxonomic distribution of proteins with vrr nuc domain a species tree will be displayed here if you enable javascript in your browser click on the protein counts or double click on taxonomic names to display all proteins containing vrr nuc domain in the selected taxonomic class embl send comments to ivica letunic
http://smart.embl-heidelberg.de/smart/complete_tree.cgi?ID=VRR_NUC
*  Treefinder
{{Infobox Software name = TreeFinder developer = Gangolf Jobb latest release version = march2011 latest release date =. A platform-independent graphical environment integrates a standard suite of analyses: phylogeny reconstruction, bootstrap analysis, model selection, hypothesis testing, tree calibration, manipulation of trees and sequence data. Result trees are displayed and can then be saved as a reconstruction report, which may serve as an input for further analysis, for example hypothesis testing. The report contains all information about the tree and the models used. The software supports a broad collection of models of sequence evolution. The June 2008 release implements 7 models of nucleotide substitution HKY, TN, J1, J2, J3 = TIM, TVM, GTR, 14 empirical models of amino acid substitution BLOSUM, cpREV, Dayhoff, JTT, LG, mtArt, mtMam, mtREV, PMB, rtREV, betHIV, witHIV, VT, WAG, 4 substitution models of structured rRNA bactRNA, eukRNA, euk23RNA, mitoRNA, the 6-state "Dayhoff Groups" ...
https://en.wikipedia.org/wiki/Treefinder
*  Human mitochondrial molecular clock
... Estimating based on AMH archaeology Estimating based on CHLCA Early, HVR, sequence-based methods Coding region sequence based methods Inter-comparing rates and studies Notes Footnotes References. The rate at which mutations accumulate in coding and non-coding region s of the genome also differs as mutations in the coding region are subject to purifying selection. For this reason, some studies avoid coding region or synonymous mutations when calibrating the molecular clock. Pedigree methods estimate the mutation rate by comparing the mtDNA sequences of a sample of parent/offspring pairs or analyzing mtDNA sequences of individuals from a deep-rooted genealogy. Phylogeny based methods are estimated by first reconstructing the haplotype of the most recent common ancestor MRCA of a sample of two or more genetic lineages. The human mutation rate is usually estimated by comparing the sequences of modern humans and chimpanzees and then reconstructing the ancestral ...
https://en.wikipedia.org/wiki/Human_mitochondrial_molecular_clock
*  blogzilly: In Light of Recent Events
... In Light of Recent Events. Unfortunately, the post I wanted to get to today will have to wait for another time. This happens when you have a youngster with multiple disabilities, one of them related to aggressive behaviors, in the public school system, and you get phone calls that suck you into it's vortex away from your job and away from other things you may have going on. I have a LOT to catch you people up on. Today. Carter was home sick, time slipped out of my hands, and by the time I had to watch the kids at night Jen works some late night shifts now ...well, I never am comfortable in the shower if Bennett is here without other supervision. Like putting on a nice worn-in old coat and finding a crisp $50 bill in it from the winter before. I can already see I am going to feel much more relaxed this year But yeah...we still have major communication delays and stuff like that out the wazoo. In fact, even though a lot of stuff has changed in a year. Let's see...I've covered being smelly and unwashed, ...
http://blogzilly.blogspot.com/2014/02/in-light-of-recent-events.html
*  Debian -- Details of package phyml in wheezy
... / Packages / wheezy oldstable / science / phyml. package names descriptions source package names package contents. all options. Links for phyml. Homepage Similar packages: fasttree. PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences. It provides a wide range of options that were designed to facilitate standard phylogenetic analyses. The main strengths of PhyML lies in the large number of substitution models coupled to various options to search the space of phylogenetic tree topologies, going from very fast and efficient methods to slower but generally more accurate approaches. It also implements two methods to evaluate branch supports in a sound statistical framework the non-parametric bootstrap and the approximate likelihood ratio test. PhyML was designed to process moderate to large data sets. In theory, alignments with up to 4,000 sequences 2,000,000 character-long can be analyzed. In ...
https://packages.debian.org/nl/wheezy/ia64/phyml
*  Systematics of Green Coccoid Algae: the Genus Bracteacoccus - EEBedia
... Systematics of Green Coccoid Algae: the Genus Bracteacoccus From EEBedia Revision as of 15:59, 29 September 2008 by KarolinaFucikova. diff ← Older revision. Latest revision diff. Newer revision → diff. Jump to: navigation, search Karolina Fučíková L. Green algae Chlorophyta are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences nuclear gene as well as rbcL sequences chloroplast, protein-coding gene. Like other coccoid genera, Bracteacoccus has very simple morphology and therefore few characters to ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_of_Green_Coccoid_Algae:_the_Genus_Bracteacoccus&oldid=8372
*  Systematics of Green Coccoid Algae: the Genus Bracteacoccus - EEBedia
... Systematics of Green Coccoid Algae: the Genus Bracteacoccus From EEBedia Revision as of 22:09, 27 April 2008 by KarolinaFucikova. Talk. contribs. diff ← Older revision. Latest revision diff. Newer revision → diff. Jump to: navigation, search Karolina Fucikova L. Lewis Lab. Green algae Chlorophyta are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences nuclear gene as well as rbcL sequences chloroplast, protein-coding gene. Phylogeny obtained from the sequence data can be subsequently ...
http://hydrodictyon.eeb.uconn.edu/eebedia/index.php?title=Systematics_of_Green_Coccoid_Algae:_the_Genus_Bracteacoccus&oldid=6391
*  The Tree of Life: Now this is my kind of meeting
4 days ago from Tweetie phylogenomics Andrew Roger at #CIFAR is talking about the origin and evolution of mitochondria and related organelles 4 days ago from TwitterFon phylogenomics Joel Dacks at #CIFAR is talking about evolution of eukaryotic membrane traffiicking how it is about "more than just eating" 4 days ago from TwitterFon JATetro @phylogenomics Will there be a proceedings or at least a review of the meeting. #CIFAR 4 days ago from Seesmic Desktop phylogenomics Tom Cavalier-Smith at #CIFAR is one of the few people who can really mix molecar phylogenetics and function/morphology for microbial euks 4 days ago from TwitterFon phylogenomics Listening to THE Tom Cavalier-Smith talking about eukaryotic evolution at #CIFAR - I don't always agree with him but he still rocks 4 days ago from TwitterFon phylogenomics Yan Boucher at #CIFAR is talking about "the life aquatic - vibrio an their mobile gene pool" - looking at lateral transfer recombination 4 days ago from TwitterFon matthewherper RT @phylogenomics ...
http://phylogenomics.blogspot.com/2009/06/now-this-is-my-kind-of-meeting.html
*  Predoc05 Practical Answers
No - and yes. These proteins cannot be homologous. Are there SM-like proteins found in Archaea. Good low P-values are reliable but actually there are many SM proteins, with weak P-values and still others that are not detected at all. So the P-values are not reliable for the more divergent but related sequences. Yes they are strong. They are all common domains. Are there structures for any of these domains. Yes, many have been found in kinase domains for example. Do you think this protein has especially many or few domains. There are many proteins with just a few domains but also many proteins with huge numbers of domains. This protein is made of only two kinds of domain - but has more than 50 of them. Exploring order/disorder with Globplot Questions and Answers Why does GlobPlot not slide a fixed window length over the sequences. But the graph indicates that these regions have mainly globular preference. These are all splendid proteins to explore with GlobPlot. Are there any annotated motifs. ...
http://embl.de/~seqanal/courses/predoc05/predoc05.answers.html
*  bernard SERIN - Member profile - Famille - MyHeritage
... You are not logged in Log in Sign up. You are currently not logged in as a member of MyHeritage. Log in or Sign up. Famille. You are not logged in Log in. Sign up. Site members Family tree. Family tree. Manage trees Photos. Family photos. Search photos Apps. MyHeritage for mobile. Family Tree Builder. Search all records. Birth, Marriage & Death. Census & Voter Lists. Family Trees. Immigration & Travel Hire a researcher. DNA tests. Members. bernard SERIN. Viewed this profile 0000236. bernard SERIN. bernard is a member of the site Famille. Other site memberships by number of visits Famille Caradec LeTessier Member, since June 23 2011. Ocio Costales Web Site Member, since Sep 3 2012. sylvie Web Site Member, since Nov 13 2012. Fradin Web Site Member, since Mar 2 2011. Family history Web Site Member, since July 16 2011. Boulanger Web Site Member, since Dec 19 2011. DENHAUT Web Site Member, since Apr 23 2012. DEMARZO Web Site Member, since Sep 4 2015. SALAFA Web Site Member, since July 18 2015. Bosse ...
http://myheritage.com/member-46601113_74865261/bernard-serin
*  SC-500E Single Event Stopwatch
sc e single event stopwatch my account log in items view cart men s swim gear women s swim gear team swim gear kids swim gear swim equipment swim accessories clearance items team login shop by brand featured products search products many thanks jeannie your customer service is top notch i wouldn t hesitate to order from you again jorie centerville oh splashwear sc e silent and audible single event stopwatch sc e silent and audible single event stopwatch can be used error free by anyone for accurate results item robic our price quantity volume discounts available of items price product details one step timing for all events start stop reset operation second resolution to hours audible beep confirmation or silent operation water resistant to meters break away safety lanyard helps prevent accidents promotes safe use one year warranty lithium batter cr other items you may like oslo w dual stopwatch countdown timer robic sc w heat stress comfort index stopwatch robic sc w dual memory speed and chronograph ...
http://swimmerstuff.com/sc500e-single-event-stopwatch-14_1515_p.aspx
*  Tinton Falls, NJ Apartments for Rent - 64 Apartments | Rent.com®
Tinton Falls, NJ Apartments for Rent - 64 Apartments. Apartments for Rent in Tinton Falls, NJ Local Info 64 Properties. 333 Tinton Falls, NJ 07753 $1745 - $2205 1-3 Beds 1-2 Baths 732 481-2168 Check Availability. 216 Units 1-3 Beds 1-2 Baths View More Info Current Rent Specials. Sea Verge Long Branch, NJ 07740 $1430 - $3395 0-2 Beds 1-2 Baths 732 734-0157 Check Availability. 126 Units 0-2 Beds 1-2 Baths View More Info Current Rent Specials. 18 Long Branch, NJ 07740 $1400 - $4415 0-3 Beds 1-2 Baths 732 443-1255 Check Availability. 283 Units 0-3 Beds 1-2 Baths View More Info Current Rent Specials. 412 Units 1-2 Beds 1 Bath View More Info Current Rent Specials. 108 Units 1-2 Beds 1 Bath View More Info Current Rent Specials. 229 West Long Branch, NJ 07764 $1740 - $2665 1-3 Beds 1-2 Baths 732 603-1189 Check Availability. 2 Long Branch, NJ 07740 $1160 - $1585 1-2 Beds 1 Bath 732 963-0001 Check Availability. 8 West End, NJ 07740 $1190 - $1685 1-2 Beds 1 Bath 732 963-2988 Check Availability. Monmouth Beach Village ...
http://rent.com/new-jersey/tinton-falls-apartments/2-21664
*  Sequence data and cladistics
... agneta guillemot agneta guillemot at historia umu se tue may est previous message re dna from formalin fixed specimen next message sequence data and cladistics messages sorted by i have a question to systematicists concerning molecular sequences and it s application in cladistic analyses the question is as follows has anyone ever been able to prove anything in a true cladistic analysis with sequence data from proteins or dna i m not interested in talk about molecular clocks and what they are presumed to have proved concerning the relationships of different taxa only in true cladistics what i want to see with my own eyes are unique sequences in dna or proteins not single substitutions of an amino acid or a base pair shared by the taxa you want group together while the other candidates for inclusion into this group have the primitive sequence as determined by outgroup comparison to you who knows anything about this please include in your reply ...
http://bio.net/bionet/mm/mol-evol/1995-May/002776.html
*  .. Phylogenetic trees from 16S rRNA .. Two-dimensional clustering .. Concluding remarks .. Group wo
XML file. We have provided a template for this file, and shall add only a section defining which genomes to be compared. This will depend on who has finished the gene prediction and translation ;- Build the configuration This is done by the scell script make-bm-config.csh - feel free to examine it using less. The scripts simply checks who has finished the *.proteins.fsa file and then build the configuration file accordingly. csh make-bm-config.csh blastmatrix.head.xml > blastmatrix.xml less blastmatrix.xml Running blast matrix program Running the BLAST matrix program scales badly with the number of proteomes n 2 and therefor takes a long time to finish for all your genomes. Luckily the program features a caching system which enables it to reuse results from searches it has already performed. For those of you who are interrested, the program uses MD5 checksums of the input proteomes to keep track of the results - this is a very convinient way to keep track of changes in large data files. We have primed ...
http://cbs.dtu.dk/courses/thaiworkshop08/docs/m16.php?grp=stud111
*  PLOS ONE: Distinct Patterns of HIV-1 Evolution within Metastatic Tissues in Patients with Non-Hodgki
Article-Level Metrics. View. Sum of PLOS and PubMed Central page views and downloads. Open Access Peer-reviewed Research Article. Article. Similar results were found in both patients: 1 high-resolution phylogenetic analysis showed a significant degree of compartmentalization between lymphoma and non-lymphoma viral sub-populations while viral sub-populations from lymph nodes appeared to be intermixed within sequences from tumor and non-tumor tissues, 2 a 100-fold increase in the effective HIV population size in tumor versus non-tumor tissues was associated with the emergence of lymphadenopathy and aggressive metastatic ARL, and 3 HIV gene flow among lymph nodes, normal and metastatic tissues was non-random. Overall, the results clearly demonstrated that the HIV strains within tumor associated macrophages in both subjects belonged to a unique viral population that was phylogenetically distinct from the strains infecting macrophages and T cells in non-tumor tissues. To address this hypothesis, HIV-1 rate ...
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008153
*  human biology - Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of
... HIV. - Biology Stack Exchange. current community. chat blog. Biology. . Biology Meta. your communities. Sign up or log in to customize your list. more stack exchange communities. Stack Exchange. Inbox. Reputation and Badges. sign up log in tour. help. Tour Start here for a quick overview of the site. Help Center Detailed answers to any questions you might have. Meta Discuss the workings and policies of this site. Biology Questions. Tags. Users. Badges. Unanswered. Ask Question. Sign up. Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. It's 100% free, no registration required. Are homozygous carriers of the CCR5-Δ32 allele fully immune to all known strains of HIV. up vote 10 down vote favorite. Or is there documented evidence of even one homozygous carrier contracting HIV and staying infected. human-biology genetics virology hiv share. improve this question. edited Jan 12 '13 at 11:20. Rory M 8,697. 5 34. 78. asked Feb 10 '12 at 19:02. mring 883. ...
http://biology.stackexchange.com/questions/975/are-homozygous-carriers-of-the-ccr5-Δ32-allele-fully-immune-to-all-known-strains/1020
*  The Protein Family Tree
... . The Protein Family Tree How can the flood of human genomic data be gainfully employed. The first step is using sequence data to determine 3-D protein structure. But how can scientists wade efficiently through this massive information to solve hundreds of thousands of proteins that remain unsolved. A series of software tools, some of them developed at PSC, make it possible to search databases and classify proteins in family groups that reflect the evolutionary relationships that select for protein function. PSC and University of Pittsburgh scientists have exhaustively analyzed the relationships among a family of enzymes called aldehyde dehydrogenase. Found in nearly every living thing, ALDH in mammals protects the body from toxic compounds. In this graphical representation of the ALDH molecular structure top, right, colors represent amino-acid groups that are "highly conserved" - they remain essentially the same in nearly all species of the enzyme. The logic of ...
http://psc.edu/science/2001/highlights/the_protein_family_tree.html
*  Recently Active 'bioinformatics' Questions - Biology Stack Exchange
Recently Active 'bioinformatics' Questions - Biology Stack Exchange. current community. chat blog. Biology. . Biology Meta. your communities. Sign up or log in to customize your list. more stack exchange communities. Stack Exchange. Inbox. Reputation and Badges. sign up log in tour. help. Tour Start here for a quick overview of the site. Help Center Detailed answers to any questions you might have. Meta Discuss the workings and policies of this site. Biology Questions. Tags. Users. Badges. Unanswered. Ask Question. Tagged Questions info newest frequent votes active unanswered. Bioinformatics connects life sciences and quantitative sciences, typically involving the application of software and algorithms to solve computationally intensive questions, such as those in genomics, sequence analysis, and systems biology. Questions tagged Bioinformatics should have a direct ... learn more. top users. synonyms 1. 3 votes. 2 answers. 83 views. Do the bacterial species X, Y, Z code for proteins A, B, C. ...
http://biology.stackexchange.com/questions/tagged/bioinformatics?sort=active&pageSize=15
*  Take The Which Lost Character Are You Test | OkCupid
Take The Which Lost Character Are You Test. OkCupid. OkCupid. Join the best free dating site on Earth. Sign in. Sign up. The Which Lost Character Are You Test Member Tests 0. Staff Tests 0. Test 0. Take this test. Danielle. You've been stuck on that damn island for so long you don't know what's going on anymore. Take The Which Lost Character Are You Test See more tests. If you don't, I will kill one of them. Oh, and Charlie, I will kill you last." You are Ethan Ro... Read more Danielle "You have three choices: run, hide or die." You are Danielle Rosseau, the French woman. You're not the most social person on the island, but you don't mind. As long as yo... Read more Locke "You're not going crazy, Jack. Crazy people don't think they're getting crazy. You are a good worker and p... Read more Claire "Don't talk to me about the baby. You are a very kind and caring person. It's gonna be a while before you're going to want to give me a piggy back ride." Dude, you are Hurley. You are a kind s... Read more Claire* ...
http://okcupid.com/quizzy/results?quizzyid=5052228135609532493&resultid=4
*  TIGR03266
... . TIGRFAMs. JCVI Home. TIGRFAMs Home. Genome Properties. TIGRFAMs Home. TIGRFAMs Terms. TIGRFAMs Complete Listing. TIGRFAMs FTP site. TIGRFAMs Resources. TIGR03266 Seed Alignment. HMM Summary Page: TIGR03266. Accession. TIGR03266. Name. methan mark 1. Function. putative methanogenesis marker protein 1. Trusted Cutoff. 365.00. Domain Trusted Cutoff. 365.00. Noise Cutoff. 265.00. Domain Noise Cutoff. 265.00. Isology Type. hypoth equivalog. HMM Length. 376. Author. Haft DH. Entry Date. Jan 16 2007 4:43PM. Last Modified. May 9 2011 8:01PM. Comment. Members of this protein family represent a distinct clade among the larger set of proteins that belong to families TIGR00702 and PF02624. Proteins from this clade are found in genome sequence if and only if the species sequenced is one of the methanogens. All methanogens belong to the archaea; some but not all of those sequenced are hyperthermophiles. This protein family was detected by the method of partial phylogenetic profiling see Haft, ...
http://jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR03266
*  SMART: DUF1220 domain annotation
... CHROMA format CLUSTALW format MSF format FASTA format PIR format. There are 2239 DUF1220 domains in 453 proteins in SMART's nrdb database. Click on the following links for more information. Evolution species in which this domain is found Taxonomic distribution of proteins containing DUF1220 domain. The complete taxonomic breakdown of all proteins with DUF1220 domain is also avaliable. Click on the protein counts, or double click on taxonomic names to display all proteins containing DUF1220 domain in the selected taxonomic class. Dumas L, Sikela JM DUF1220 domains, cognitive disease, and human brain evolution. 2009; 74 : 375-82 Display abstract We have established that human genome sequences encoding a novel protein domain, DUF1220, show a dramatically elevated copy number in the human lineage >200copies in humans vs. Copy-number variations CNVs in the 1q21.1 region, where mostDUF1220 sequences map, have now been implicated in numerous diseases associatedwith cognitive dysfunction, ...
http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN=DUF1220&BLAST=DUMMY
*  Bio-IT World
New studies of the bacterium that causes anthrax will involve “a lot more sequencing, phylogenetic context, and developing molecular signatures for strains,” says P. New phylogenetic trees could also provide better analytical tools for predicting the functions of unknown proteins. In new findings, Keim and colleagues at Los Alamos and TIGR have recently identified differences among several Ames samples. TIGR intends to sequence the genomes of as many as 14 anthrax strains from around the world, far more than have been sequenced for any other species. “What is needed is an archive containing a fair number of samples and a strategy for going from sequencing of multiple, whole genomes to finding regions containing highly specific molecular signatures,” White says. The Los Alamos group is developing a process for establishing such signatures in any pathogen based on a molecular taxonomic approach, which White describes as the “rational design of DNA signatures.” The development ...
http://bio-itworld.com/archive/040702/anthrax/

Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Hyperparameter: In Bayesian statistics, a hyperparameter is a parameter of a prior distribution; the term is used to distinguish them from parameters of the model for the underlying system under analysis.DNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Mac OS X Server 1.0Coles PhillipsCS-BLASTDecoding methods: In coding theory, decoding is the process of translating received messages into codewords of a given code. There have been many common methods of mapping messages to codewords.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Large ornamented Ediacaran microfossil: Large ornamented Ediacaran microfossils (LOEMs) are microscopic acritarchs, usually over 100 μm in diameter, which are common in sediments of the Ediacaran period, . They largely disappear from the Ediacaran fossil record before , roughly coeval with the origin of the Ediacara biota.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Vladimir Andreevich Markov: Vladimir Andreevich Markov (; May 8, 1871 – January 18, 1897) was a Russian mathematician, known for proving the Markov brothers' inequality with his older brother Andrey Markov. He died of tuberculosis at the age of 25.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Haplogroup L0 (mtDNA)Amplified Ribosomal DNA Restriction Analysis: Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length polymorphism) to the gene encoding the small (16s) ribosomal subunit of bacteria. The technique involves an enzymatic amplification using primers directed at the conserved regions at the ends of the 16s gene, followed by digestion using tetracutter Restriction enzymes.Genetic variation: right|thumbMonte Carlo methods for option pricing: In mathematical finance, a Monte Carlo option model uses Monte Carlo methods Although the term 'Monte Carlo method' was coined by Stanislaw Ulam in the 1940s, some trace such methods to the 18th century French naturalist Buffon, and a question he asked about the results of dropping a needle randomly on a striped floor or table. See Buffon's needle.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.List of sequenced eukaryotic genomesCommunity Fingerprinting: Community fingerprinting refers to a set of molecular biology techniques that can be used to quickly profile the diversity of a microbial community. Rather than directly identifying or counting individual cells in an environmental sample, these techniques show how many variants of a gene are present.Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Ligation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.Glossary of scientific names: A glossary of the meaning of scientific names of living things, viruses and prions .Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Global microbial identifier: The genomic epidemiological database for global identification of microorganisms or global microbial identifier (GMI) is a platform for storing whole genome sequencing (WGS) data of microorganisms, for the identification of relevant genes and for the comparison of genomes to detect and track-and-trace infectious disease outbreaks and emerging pathogens. The database holds two types of information: 1) genomic information of microorganisms, linked to, 2) metadata of those microorganism such as epidemiological details.Phylogeography: Phylogeography is the study of the historical processes that may be responsible for the contemporary geographic distributions of individuals. This is accomplished by considering the geographic distribution of individuals in light of the patterns associated with a gene genealogy.Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.NADH-QPanmixia: Panmixia (or panmixis) means random mating.King C and Stanfield W.Thermal cyclerChromosome regionsMicrobiota: A microbiota is "the ecological community of commensal, symbiotic and pathogenic microorganisms that literally share our body space". Joshua Lederberg coined the term, emphasising the importance of microorganisms inhabiting the human body in health and disease.DNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Immersive technologyLibrary (biology): In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated).Exome: The exome is the part of the genome formed by exons, the sequences which when transcribed remain within the mature RNA after introns are removed by RNA splicing. It consists of all DNA that is transcribed into mature RNA in cells of any type as distinct from the transcriptome, which is the RNA that has been transcribed only in a specific cell population.Cancer Genome Project: The Cancer Genome Project, based at the Wellcome Trust Sanger Institute, aims to identify sequence variants/mutations critical in the development of human cancers. Like The Cancer Genome Atlas project within the United States, the Cancer Genome Project represents an effort in the War on Cancer to improve cancer diagnosis, treatment, and prevention through a better understanding of the molecular basis of this disease.MoniliellaConference and Labs of the Evaluation Forum: The Conference and Labs of the Evaluation Forum (formerly Cross-Language Evaluation Forum), or CLEF, is an organization promoting research in multilingual information access (currently focusing on European languages). Its specific functions are to maintain an underlying framework for testing information retrieval systems and to create repositories of data for researchers to use in developing comparable standards.SciDBOpen reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).Health geography: Health geography is the application of geographical information, perspectives, and methods to the study of health, disease, and health care.WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Lempel–Ziv–Oberhumer: Lempel–Ziv–Oberhumer (LZO) is a lossless data compression algorithm that is focused on decompression speed.Exogenous bacteria: Exogenous bacteria are microorganisms introduced to closed biological systems from the external world. They exist in aquatic and terrestrial environments, as well as the atmosphere.Lasiodiplodia: Lasiodiplodia is a genus of fungi in the family Botryosphaeriaceae. There are 21 species.Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Selection (relational algebra): In relational algebra, a selection (sometimes called a restriction to avoid confusion with SQL's use of SELECT) is a unary operation written asHuman Proteinpedia: Human Proteinpedia is a portal for sharing and integration of human proteomic data,.Kandasamy et al.Calculator: An electronic calculator is a small, portable electronic device used to perform both basic operations of arithmetic and complex mathematical operations.AmborellaCodon Adaptation Index: The Codon Adaptation Index (CAI) is the most widespread technique for analyzing Codon usage bias. As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.Intergenic region: An Intergenic region (IGR) is a stretch of DNA sequences located between genes. Intergenic regions are a subset of Noncoding DNA.Transfer-messenger RNA: Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. The tmRNA forms a ribonucleoprotein complex (tmRNP) together with Small Protein B (SmpB), Elongation Factor Tu (EF-Tu), and ribosomal protein S1.Stromule: A stromule is a microscopic structure found in plant cells. Stromules (stroma-filled tubules) are highly dynamic structures extending from the surface of all plastid types, including proplastids, chloroplasts, etioplasts, leucoplasts, amyloplasts, and chromoplasts.MT-RNR2: Mitochondrially encoded 16S RNA (often abbreviated as 16S) is a mitochondrial ribosomal RNA (rRNA) that in humans is encoded by the MT-RNR2 gene. The MT-RNR2 gene also encodes the Humanin polypeptide that has been the target of Alzheimer's disease research.

(1/277092) Novel regulation of the homeotic gene Scr associated with a crustacean leg-to-maxilliped appendage transformation.

Homeotic genes are known to be involved in patterning morphological structures along the antero-posterior axis of insects and vertebrates. Because of their important roles in development, changes in the function and expression patterns of homeotic genes may have played a major role in the evolution of different body plans. For example, it has been proposed that during the evolution of several crustacean lineages, changes in the expression patterns of the homeotic genes Ultrabithorax and abdominal-A have played a role in transformation of the anterior thoracic appendages into mouthparts termed maxillipeds. This homeotic-like transformation is recapitulated at the late stages of the direct embryonic development of the crustacean Porcellio scaber (Oniscidea, Isopoda). Interestingly, this morphological change is associated with apparent novelties both in the transcriptional and post-transcriptional regulation of the Porcellio scaber ortholog of the Drosophila homeotic gene, Sex combs reduced (Scr). Specifically, we find that Scr mRNA is present in the second maxillary segment and the first pair of thoracic legs (T1) in early embryos, whereas protein accumulates only in the second maxillae. In later stages, however, high levels of SCR appear in the T1 legs, which correlates temporally with the transformation of these appendages into maxillipeds. Our observations provide further insight into the process of the homeotic leg-to-maxilliped transformation in the evolution of crustaceans and suggest a novel regulatory mechanism for this process in this group of arthropods.  (+info)

(2/277092) The Drosophila kismet gene is related to chromatin-remodeling factors and is required for both segmentation and segment identity.

The Drosophila kismet gene was identified in a screen for dominant suppressors of Polycomb, a repressor of homeotic genes. Here we show that kismet mutations suppress the Polycomb mutant phenotype by blocking the ectopic transcription of homeotic genes. Loss of zygotic kismet function causes homeotic transformations similar to those associated with loss-of-function mutations in the homeotic genes Sex combs reduced and Abdominal-B. kismet is also required for proper larval body segmentation. Loss of maternal kismet function causes segmentation defects similar to those caused by mutations in the pair-rule gene even-skipped. The kismet gene encodes several large nuclear proteins that are ubiquitously expressed along the anterior-posterior axis. The Kismet proteins contain a domain conserved in the trithorax group protein Brahma and related chromatin-remodeling factors, providing further evidence that alterations in chromatin structure are required to maintain the spatially restricted patterns of homeotic gene transcription.  (+info)

(3/277092) The homeobox gene Pitx2: mediator of asymmetric left-right signaling in vertebrate heart and gut looping.

Left-right asymmetry in vertebrates is controlled by activities emanating from the left lateral plate. How these signals get transmitted to the forming organs is not known. A candidate mediator in mouse, frog and zebrafish embryos is the homeobox gene Pitx2. It is asymmetrically expressed in the left lateral plate mesoderm, tubular heart and early gut tube. Localized Pitx2 expression continues when these organs undergo asymmetric looping morphogenesis. Ectopic expression of Xnr1 in the right lateral plate induces Pitx2 transcription in Xenopus. Misexpression of Pitx2 affects situs and morphology of organs. These experiments suggest a role for Pitx2 in promoting looping of the linear heart and gut.  (+info)

(4/277092) Mrj encodes a DnaJ-related co-chaperone that is essential for murine placental development.

We have identified a novel gene in a gene trap screen that encodes a protein related to the DnaJ co-chaperone in E. coli. The gene, named Mrj (mammalian relative of DnaJ) was expressed throughout development in both the embryo and placenta. Within the placenta, expression was particularly high in trophoblast giant cells but moderate levels were also observed in trophoblast cells of the chorion at embryonic day 8.5, and later in the labyrinth which arises from the attachment of the chorion to the allantois (a process called chorioallantoic fusion). Insertion of the ROSAbetageo gene trap vector into the Mrj gene created a null allele. Homozygous Mrj mutants died at mid-gestation due to a failure of chorioallantoic fusion at embryonic day 8.5, which precluded formation of the mature placenta. At embryonic day 8.5, the chorion in mutants was morphologically normal and expressed the cell adhesion molecule beta4 integrin that is known to be required for chorioallantoic fusion. However, expression of the chorionic trophoblast-specific transcription factor genes Err2 and Gcm1 was significantly reduced. The mutants showed no abnormal phenotypes in other trophoblast cell types or in the embryo proper. This study indicates a previously unsuspected role for chaperone proteins in placental development and represents the first genetic analysis of DnaJ-related protein function in higher eukaryotes. Based on a survey of EST databases representing different mouse tissues and embryonic stages, there are 40 or more DnaJ-related genes in mammals. In addition to Mrj, at least two of these genes are also expressed in the developing mouse placenta. The specificity of the developmental defect in Mrj mutants suggests that each of these genes may have unique tissue and cellular activities.  (+info)

(5/277092) A Drosophila doublesex-related gene, terra, is involved in somitogenesis in vertebrates.

The Drosophila doublesex (dsx) gene encodes a transcription factor that mediates sex determination. We describe the characterization of a novel zebrafish zinc-finger gene, terra, which contains a DNA binding domain similar to that of the Drosophila dsx gene. However, unlike dsx, terra is transiently expressed in the presomitic mesoderm and newly formed somites. Expression of terra in presomitic mesoderm is restricted to cells that lack expression of MyoD. In vivo, terra expression is reduced by hedgehog but enhanced by BMP signals. Overexpression of terra induces rapid apoptosis both in vitro and in vivo, suggesting that a tight regulation of terra expression is required during embryogenesis. Terra has both human and mouse homologs and is specifically expressed in mouse somites. Taken together, our findings suggest that terra is a highly conserved protein that plays specific roles in early somitogenesis of vertebrates.  (+info)

(6/277092) Requirement of a novel gene, Xin, in cardiac morphogenesis.

A novel gene, Xin, from chick (cXin) and mouse (mXin) embryonic hearts, may be required for cardiac morphogenesis and looping. Both cloned cDNAs have a single open reading frame, encoding proteins with 2,562 and 1,677 amino acids for cXin and mXin, respectively. The derived amino acid sequences share 46% similarity. The overall domain structures of the predicted cXin and mXin proteins, including proline-rich regions, 16 amino acid repeats, DNA-binding domains, SH3-binding motifs and nuclear localization signals, are highly conserved. Northern blot analyses detect a single message of 8.9 and 5.8 kilo base (kb) from both cardiac and skeletal muscle of chick and mouse, respectively. In situ hybridization reveals that the cXin gene is specifically expressed in cardiac progenitor cells of chick embryos as early as stage 8, prior to heart tube formation. cXin continues to be expressed in the myocardium of developing hearts. By stage 15, cXin expression is also detected in the myotomes of developing somites. Immunofluorescence microscopy reveals that the mXin protein is colocalized with N-cadherin and connexin-43 in the intercalated discs of adult mouse hearts. Incubation of stage 6 chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and an alteration of cardiac looping. The myocardium of the affected hearts becomes thickened and tends to form multiple invaginations into the heart cavity. This abnormal cellular process may account in part for the abnormal looping. cXin expression can be induced by bone morphogenetic protein (BMP) in explants of anterior medial mesoendoderm from stage 6 chick embryos, a tissue that is normally non-cardiogenic. This induction occurs following the BMP-mediated induction of two cardiac-restricted transcription factors, Nkx2.5 and MEF2C. Furthermore, either MEF2C or Nkx2.5 can transactivate a luciferase reporter driven by the mXin promoter in mouse fibroblasts. These results suggest that Xin may participate in a BMP-Nkx2.5-MEF2C pathway to control cardiac morphogenesis and looping.  (+info)

(7/277092) Characterization of an amphioxus paired box gene, AmphiPax2/5/8: developmental expression patterns in optic support cells, nephridium, thyroid-like structures and pharyngeal gill slits, but not in the midbrain-hindbrain boundary region.

On the basis of developmental gene expression, the vertebrate central nervous system comprises: a forebrain plus anterior midbrain, a midbrain-hindbrain boundary region (MHB) having organizer properties, and a rhombospinal domain. The vertebrate MHB is characterized by position, by organizer properties and by being the early site of action of Wnt1 and engrailed genes, and of genes of the Pax2/5/8 subfamily. Wada and others (Wada, H., Saiga, H., Satoh, N. and Holland, P. W. H. (1998) Development 125, 1113-1122) suggested that ascidian tunicates have a vertebrate-like MHB on the basis of ascidian Pax258 expression there. In another invertebrate chordate, amphioxus, comparable gene expression evidence for a vertebrate-like MHB is lacking. We, therefore, isolated and characterized AmphiPax2/5/8, the sole member of this subfamily in amphioxus. AmphiPax2/5/8 is initially expressed well back in the rhombospinal domain and not where a MHB would be expected. In contrast, most of the other expression domains of AmphiPax2/5/8 correspond to expression domains of vertebrate Pax2, Pax5 and Pax8 in structures that are probably homologous - support cells of the eye, nephridium, thyroid-like structures and pharyngeal gill slits; although AmphiPax2/5/8 is not transcribed in any structures that could be interpreted as homologues of vertebrate otic placodes or otic vesicles. In sum, the developmental expression of AmphiPax2/5/8 indicates that the amphioxus central nervous system lacks a MHB resembling the vertebrate isthmic region. Additional gene expression data for the developing ascidian and amphioxus nervous systems would help determine whether a MHB is a basal chordate character secondarily lost in amphioxus. The alternative is that the MHB is a vertebrate innovation.  (+info)

(8/277092) Mechanisms of GDF-5 action during skeletal development.

Mutations in GDF-5, a member of the TGF-beta superfamily, result in the autosomal recessive syndromes brachypod (bp) in mice and Hunter-Thompson and Grebe-type chondrodysplasias in humans. These syndromes are all characterised by the shortening of the appendicular skeleton and loss or abnormal development of some joints. To investigate how GDF-5 controls skeletogenesis, we overexpressed GDF-5 during chick limb development using the retrovirus, RCASBP. This resulted in up to a 37.5% increase in length of the skeletal elements, which was predominantly due to an increase in the number of chondrocytes. By injecting virus at different stages of development, we show that GDF-5 can increase both the size of the early cartilage condensation and the later developing skeletal element. Using in vitro micromass cultures as a model system to study the early steps of chondrogenesis, we show that GDF-5 increases chondrogenesis in a dose-dependent manner. We did not detect changes in proliferation. However, cell suspension cultures showed that GDF-5 might act at these stages by increasing cell adhesion, a critical determinant of early chondrogenesis. In contrast, pulse labelling experiments of GDF-5-infected limbs showed that at later stages of skeletal development GDF-5 can increase proliferation of chondrocytes. Thus, here we show two mechanisms of how GDF-5 may control different stages of skeletogenesis. Finally, our data show that levels of GDF-5 expression/activity are important in controlling the size of skeletal elements and provides a possible explanation for the variation in the severity of skeletal defects resulting from mutations in GDF-5.  (+info)


human genome


  • Molecular data is simply genomic information and is acquired through human genome sequencing. (ripcitytoseoul.com)
  • SAN FRANCISCO, Tues., June 8, 2004 The National Human Genome Research Institute (NHGRI), part of the National Institutes of Health (NIH), today announced a partnership with the Melbourne-based Australian Genome Research Facility Ltd. (AGRF) to sequence the DNA of one of Australia's best-known animals: a member of the kangaroo family known as the tammar wallaby. (bio-medicine.org)
  • Comparing the human genome sequence with those of other organisms, such as the roundworm, mouse or kangaroo, enables scientists to identify regions of similarity and difference that can provide clues about the structure and function of genes vital to human health and development. (bio-medicine.org)


genomic


  • Using available genomic sequence data on coagulation factor VIII and predictive models of molecular evolution, we engineer protein variants with improved activity, stability. (pubmedcentralcanada.ca)
  • Comparing the Aegilops tauschii sequence with modern wheat allows researchers to assess genomic changes that have taken place in bread wheat since its origin approximately 8,000 years ago. (bio-medicine.org)


protein


  • In principle, this approach can be applied to any protein drug based on a conserved gene sequence. (pubmedcentralcanada.ca)
  • This inferred protein design landscape represents an unexplored avenue for protein drug optimization that is accessible through ancestral sequence reconstruction (ASR). (pubmedcentralcanada.ca)
  • ASR entails the prediction of ancient DNA and protein sequences based on information from extant sequences 8 . (pubmedcentralcanada.ca)
  • The pf16 gene product is a 57-kD protein with sequence similarity to armadillo repeat proteins ( Smith and Lefebvre, 1996 ) whose precise role in central pair structure and function has not been determined, but the C1 microtubule is unstable in demembranated pf16 axonemes. (rupress.org)
  • Activity studies of expressed chimeric UGT cDNAs have shown that the aglycone binding domain is likely to be seated within the first 298 amino acids of the N terminus of the protein, presumably in the region amino acids 55 to 180, a region with least homology of primary sequence between the UGT isoforms ( Mackenzie, 1990 ). (aspetjournals.org)
  • Whereas FKBP12 is cytosolic, FKBP13 is a membrane-associated protein, possessing an NH 2 -terminal signal sequence and COOH-terminal RTEL motif, which are believed to play roles in protein targeting and ER retention, respectively ( 37 ). (rupress.org)


phylogeny


  • In contrast to ortholog scanning, it provides a higher-resolution mapping through comparisons of sequential phylogeny branches, and infers novel sequences with high potential for intended biomolecular functions as they are predicted to have once existed. (pubmedcentralcanada.ca)


biology


  • Van Houten, a double major in mathematics and biochemistry and molecular biology while at Wooster, spoke about RNA sequencing, a process that provides access to information about gene expression. (wooster.edu)
  • The topic was of keen interest to many at the workshop, including Allison Grenell, a rising junior biochemistry and molecular biology major at Wooster. (wooster.edu)
  • Our research focuses on computational approaches to problems in molecular biology. (nanohub.org)
  • MicroRNAs (miRNAs) are a new class of regulatory molecules that were discovered through investigation of the RNAi pathway, and have become one of the hottest topics in molecular biology today. (edu.au)


proteins


  • Taken together, these data suggested that FKBP13 may function as an ER molecular chaperone, which binds to and catalyzes the folding and/or assembly of proteins in the ER. (rupress.org)


cellular and molecular


  • To develop cellular and molecular tools to support development of vaccines against intracellular pathogens of sheep, we have undertaken a molecular genetic analysis of four distinct ovine MHC haplotypes carried by two heterozygous Blackface rams. (cut.ac.cy)


genetics


  • This sequencing effort has yielded important information that will accelerate wheat genetics and breeding and help us better understand wheat evolution," Dvorak said. (bio-medicine.org)


novel


  • We have identified 12 novel class I transcripts and used a class I sequence-specific genotyping system to assign each of these transcripts to individual haplotypes. (cut.ac.cy)
  • We also strive to understand how sequences involved in gene regulation have evolved, and how such evolutionary dynamics may inform the discovery of novel regulatory sequences. (nanohub.org)
  • We present a novel method for detecting mass-extinction events from phylogenies estimated from molecular sequence data. (biorxiv.org)


gene expression


  • We approach the subject through an integrated analysis of DNA sequence and gene expression data. (nanohub.org)


species


  • We 1 - 4 and others 5 have shown that extant FVIII orthologs have molecular, cellular and immune recognition properties that vary between species. (pubmedcentralcanada.ca)
  • To aid the sequence assembly of bread wheat, Dvorak and the UC Davis researchers have worked with scientists at the U.S. Department of Agriculture's Agricultural Research Service and with scientists at two other U.S. institutions on sequencing of the genome of the parent species Aegilops tauschii the source of the bread wheat D genome. (bio-medicine.org)


Analyses


  • Analyses of rbcL sequence data and morphological features show that Theaceae s.l. does not form a natural family (APG 2002) and is treated here in the same way as the subfamily Theoideae sensu Cronquist containing the Neotropical Laplacea and the cultivated Camellia . (kew.org)


reads


  • Motivation: Oxford Nanopore's MinION device has matured rapidly and is now capable of producing over one million reads and several gigabases of sequence data per run. (biorxiv.org)
  • In the study reported in Nature, the researchers used the whole genome "shotgun sequencing" approach, which generates billions of random genome sequence "reads" and then pieces them together. (bio-medicine.org)


Scientists


  • The nature of the MinION output re-quires new tools that are easy to use by scientists with a range of computational skills and which enable quick and simple QC and data extraction from MinION runs. (biorxiv.org)
  • Intent on developing wheat varieties with higher yields and enhanced nutritional content, researchers at the University of California, Davis, have teamed up with scientists at nine other institutions in an attempt to sequence the wheat genome. (bio-medicine.org)


approach


  • Here we test an alternative approach based on ancestral sequence reconstruction. (pubmedcentralcanada.ca)
  • This new approach?the CPP on Mass Extinction Times (CoMET) model?provides an effective tool for identifying mass-extinction events from molecular phylogenies, even when the history of those groups includes more prosaic temporal variation in diversification rate. (biorxiv.org)


analysis


  • Molecular genetic analysis of the bovine MHC has revealed considerable haplotype and allelic diversity that earlier serological analysis had not detected. (cut.ac.cy)
  • Using a combination of phylogenetic analysis, haplotype and transcript expression data, we identified at least four distinct polymorphic class I MHC loci, three of which appear together in a number of combinations in individual haplotypes. (cut.ac.cy)


accessible


  • A proliferation of "Big Data" in the life sciences - as in many other fields - has created significant challenges for those who seek to analyze it, but a recent workshop at The College of Wooster helped to make the process more accessible. (wooster.edu)


Type


  • The type of kangaroo chosen for sequencing is the tammar wallaby (Macropus eugenii), a relatively small member of the kangaroo family found on islands along Australia's southern and western coasts. (bio-medicine.org)


several


  • several months ago, NHGRI approved plans to sequence a gray short-tailed, South American opossum (Monodelphis domestica). (bio-medicine.org)


team


  • The U.S. team shared the Aegilops tauschii sequences with the British team, which was assembling all three of the wheat A, B and D genomes. (bio-medicine.org)


Program


  • Wenger and others noted the importance of learning and understanding the latest software, including a program called "Galaxy," which proved to be very useful in mining and analyzing large amounts of data. (wooster.edu)


studies


  • Here, we review molecular studies of the endemic terrestrial fauna of the Hawaiian archipelago. (royalsocietypublishing.org)
  • Taxonomy has also been elucidated by molecular studies ( Achatinella snails, drosophilids). (royalsocietypublishing.org)
  • While molecular studies on Hawaiian fauna have burgeoned since the mid-1990s, much remains unknown. (royalsocietypublishing.org)
  • Pseudodominant inheritance of goitrous congenital hypothyroidism caused by TPO mutations: molecular and in silico studies. (ac.be)


high


  • It cannot be overemphasized, however, that this is just one step in the global effort to produce a high-quality draft of the bread wheat genome sequence. (bio-medicine.org)
  • He said completion of such a high-quality genome sequence for bread wheat is still a few years away and will require broad international collaboration to complete. (bio-medicine.org)


study


  • I want to go to grad school and study molecular evolution, so this workshop was very valuable for me," he said. (wooster.edu)
  • This work moves us one step closer to a comprehensive and highly detailed genome sequence for bread wheat, which along with rice and maize is one of the three pillars on which the global food supply rests," said Jan Dvorak, professor of plant sciences at UC Davis and a study co-author. (bio-medicine.org)


Major


  • The inability to sufficiently 'humanize' ortholog-hybrid molecules with xenogeneic sequences, similarly to what is done for monoclonal antibody biologics, is a major limitation of ortholog-scanning for pharmaceutical development. (pubmedcentralcanada.ca)


databases


  • The challenge for all of us is to find out how to query the databases intelligently and then apply the data to our research. (wooster.edu)


large


  • Both GUIs are capable of extracting sequence- and meta- data from large MinION da-tasets via a friendly point-and-click interface using commodity hardware. (biorxiv.org)


complex


  • UC Davis researchers aid effort to sequence the complex wh. (bio-medicine.org)


research


  • Jason Van Houten, a 2011 College of Wooster graduate and currently a research assistant at the Ohio Agricultural Research and Development Center (OARDC), makes a presentation about RNA sequencing at the Northeast Ohio Bioinformatics Workshop and Jamboree, held last week at The College of Wooster. (wooster.edu)
  • We expect the data generated by the kangaroo genome project will prove to be extremely valuable for medical research, as well as agricultural research, around the globe. (bio-medicine.org)


effective


  • The three-day event drew an enthusiastic group of more than 40 graduate and undergraduate students seeking to learn effective techniques for gathering and evaluating the data. (wooster.edu)


Results


  • These results suggest the feasibility of a subunit smallpox vaccine based on VARV antigen sequences to induce immunity against poxvirus infection. (umassmed.edu)


Securing a hospital’s information systems data is essential for the survival of the agency. What types of data?


  • Securing a hospital’s information systems data is essential for the survival of the agency. What types of data must be protected? Describe the various methods for ensuring the privacy and confidentiality of hospital information.
  • Types of data to protect: patient's private information, such as diagnosis, medications, treatments, insurance info. Patient chart. Computerized data on the patient. How to help ensure privacy: Educate nurses about turning computer screens away from public view. Password protection for all staff members. Encryption of data. Not allowing staff or workers take laptops home. Just some ideas to get you started.


What does the phrase quality data mean when referring to electronic medical records?


  • What is quality data?
  • Information that is precise and accurate. If my record lists me as a 120 year old monkey with an allergy to peanuts, then that is poor quality data. None of those things are true. Quality data is also structured. Free text like "75 year old pregnant woman with yellow skin" is not good for an EMR if you try searching for everyone with jaundice (which involves yellow skin).


What is book that explains on a molecular neurological µbiological level how antipsychotic drugs work?


  • Title of a book that explains in detail (on a molecular and neuroligical) level how psychiatric drugs have the affect that they do on the brain tissue and what the long lasting effects could be ?
  • Maybe a neuropsychiatry textbook.


Where can I find Medicare reimbursement data related to vaginal birth?


  • The hospital has charged us an insane amount, and I would like to use this data to negotiate them down. I've looked into their "charity program" and we don't qualify for that. Thanks.
  • Since you asked this on the US board I guessing you are in the US and are talking about United States Medicare, not Medicare from a different country. If so, Medicare does not have a reimbursement rate for any maternity because Medicare does not cover any maternity.


How do I start cooking with Molecular Gastronomy?


  • I have been cooking for years now, and I want to step it up to the next level and start cooking with molecular gastronomy. Where is a good place to start? Books?
  • Here: http://www.alacuisine.org/alacuisine/2004/11/molecular_gastr.html http://en.wikipedia.org/wiki/Molecular_gastronomy


What should be the sequence of exercise?


  • I watched some videos on youtube for exercise at home. Every trainer in those videos recommended to do them in the sequence shown. Well, I do a mix of excesaise shown in different videos so I want to know in which sequence I should do those exercises to get the best effect. Is there any sequence like first I should it for shoulders then biceps then triceps then chest, abs, legs and so on ?
  • In general you can have a upper body exercise on one day and lower body exercise on another day. This gives sufficient relaxation to your muscle and also do not pain very hard. I usually follow exercise from upper to lower like shoulder, biceps, triceps, fore arms, etc.


How will i sequence these exercises in my strength building routine?


  • Currently i do exercises such as push ups, dips, sit ups, bicep curls and sometimes chin ups. I can do 3 sets of 20 push ups, 2 sets of 15 dips, 3 sets of 8 bicep curls, 1 set of 35 sit ups and barely 2 reps of chin ups. can anyone tell me how will i sequence these exercises as in what after what and how long break will i take between them? a proper comprehensive answer is what i want for the best answer.
  • If these are the only exercises that you are doing, then i suggest you aim for more repetitions for your push ups and sit ups. That said, it seems like you're at the beginning stage of your strength training program, so what you are doing is alright, but not fantastic. The sequence that you should do the exercises that you are currently doing should all affect the same muscle groups (i.e. chest + triceps, back + biceps, and abs can be done separately after your main workouts). Chest + Triceps: 3 sets up push ups at a 1 minute rest interval. When you're done your push ups do your 2 sets of dips, also at a 1 minute rest interval. The same idea for your back + biceps: Chin ups and bicep curls. Chin ups/Pull ups are fantastic workouts, and they are perfect for training upper body strength, so do not skip out on doing them. If you're doing 2 normal reps now, I suggest you keep working on your chin ups/pull ups. In order to increase the amount of chin ups you can do, try doing negatives. Here's how to do a negative chin up: http://www.youtube.com/watch?v=Opr72q6NKTc


How can I receive any new data on my email on a certain drug?


  • I would like to get any online published data on a certain drug on my email as alerts, how can I do that?
  • They will not do that. That would be like asking for lawsuits...