The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.
The genetic complement of a BACTERIA as represented in its DNA.
The complete genetic complement contained in a DNA or RNA molecule in a virus.
The genetic complement of a plant (PLANTS) as represented in its DNA.
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.
The genetic complement of MITOCHONDRIA as represented in their DNA.
The complete gene complement contained in a set of chromosomes in a fungus.
The amount of DNA (or RNA) in one copy of a genome.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The genetic complement of an archaeal organism (ARCHAEA) as represented in its DNA.
The relationships of groups of organisms as reflected by their genetic makeup.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
The genetic complement of an insect (INSECTS) as represented in its DNA.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
The complete genetic complement contained in a set of CHROMOSOMES in a protozoan.
The systematic study of the complete DNA sequences (GENOME) of organisms.
The genetic complement of CHLOROPLASTS as represented in their DNA.
Any method used for determining the location of and relative distances between genes on a chromosome.
The genetic complement of a helminth (HELMINTHS) as represented in its DNA.
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).
The genetic complement of PLASTIDS as represented in their DNA.
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.
The presence of two or more genetic loci on the same chromosome. Extensions of this original definition refer to the similarity in content and organization between chromosomes, of different species for example.
A coordinated effort of researchers to map (CHROMOSOME MAPPING) and sequence (SEQUENCE ANALYSIS, DNA) the human GENOME.
Deoxyribonucleic acid that makes up the genetic material of viruses.
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.
The sequential location of genes on a chromosome.
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.
Genotypic differences observed among individuals in a population.
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.
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.
Databases devoted to knowledge about specific genes and gene products.
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.
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.
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)
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.
Processes occurring in various organisms by which new genes are copied. Gene duplication may result in a MULTIGENE FAMILY; supergenes or PSEUDOGENES.
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).
Ribonucleic acid that makes up the genetic material of viruses.
The functional hereditary units of VIRUSES.
Sequential operating programs and data which instruct the functioning of a digital computer.
The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.
Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.
The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.
Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.
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.
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.
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.
Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
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.
Deoxyribonucleic acid that makes up the genetic material of plants.
Proteins found in any species of virus.
The naturally occurring transmission of genetic information between organisms, related or unrelated, circumventing parent-to-offspring transmission. Horizontal gene transfer may occur via a variety of naturally occurring processes such as GENETIC CONJUGATION; GENETIC TRANSDUCTION; and TRANSFECTION. It may result in a change of the recipient organism's genetic composition (TRANSFORMATION, GENETIC).
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.
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)
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.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
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.
Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.
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)
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.
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.
The process of intracellular viral multiplication, consisting of the synthesis of PROTEINS; NUCLEIC ACIDS; and sometimes LIPIDS, and their assembly into a new infectious particle.
An increased tendency of the GENOME to acquire MUTATIONS when various processes involved in maintaining and replicating the genome are dysfunctional.
The functional hereditary units of BACTERIA.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
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).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The functional hereditary units of PLANTS.
The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA.
Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.
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.
The parts of a GENOME sequence that are involved with the different functions or properties of genomes as a whole as opposed to those of individual GENES.
Established cell cultures that have the potential to propagate indefinitely.
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.
Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.
In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Proteins found in any species of bacterium.
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.
The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.
Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.
Hybridization of a nucleic acid sample to a very large set of OLIGONUCLEOTIDE PROBES, which have been attached individually in columns and rows to a solid support, to determine a BASE SEQUENCE, or to detect variations in a gene sequence, GENE EXPRESSION, or for GENE MAPPING.
The process by which a DNA molecule is duplicated.
Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.
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.
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.
The co-inheritance of two or more non-allelic GENES due to their being located more or less closely on the same CHROMOSOME.
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.
The number of copies of a given gene present in the cell of an organism. An increase in gene dosage (by GENE DUPLICATION for example) can result in higher levels of gene product formation. GENE DOSAGE COMPENSATION mechanisms result in adjustments to the level GENE EXPRESSION when there are changes or differences in gene dosage.
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).
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.
Viruses whose hosts are bacterial cells.
The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Differential and non-random reproduction of different genotypes, operating to alter the gene frequencies within a population.
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.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
Nucleotide sequences repeated on both the 5' and 3' ends of a sequence under consideration. For example, the hallmarks of a transposon are that it is flanked by inverted repeats on each end and the inverted repeats are flanked by direct repeats. The Delta element of Ty retrotransposons and LTRs (long terminal repeats) are examples of this concept.
The portion of an interactive computer program that issues messages to and receives commands from a user.
Genomes of temperate BACTERIOPHAGES integrated into the DNA of their bacterial host cell. The prophages can be duplicated for many cell generations until some stimulus induces its activation and virulence.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
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.
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).
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.
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.
Deoxyribonucleic acid that makes up the genetic material of CHLOROPLASTS.
A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.
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).
A method for comparing two sets of chromosomal DNA by analyzing differences in the copy number and location of specific sequences. It is used to look for large sequence changes such as deletions, duplications, amplifications, or translocations.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Animals having a vertebral column, members of the phylum Chordata, subphylum Craniata comprising mammals, birds, reptiles, amphibians, and fishes.
Cells lacking a nuclear membrane so that the nuclear material is either scattered in the cytoplasm or collected in a nucleoid region.
The relationship between two different species of organisms that are interdependent; each gains benefits from the other or a relationship between different species where both of the organisms in question benefit from the presence of the other.
A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.
DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.
Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
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.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.
Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.
Viruses whose genetic material is RNA.
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.
Insertion of viral DNA into host-cell DNA. This includes integration of phage DNA into bacterial DNA; (LYSOGENY); to form a PROPHAGE or integration of retroviral DNA into cellular DNA to form a PROVIRUS.
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.
The functional genetic units of ARCHAEA.
A plant genus of the family POACEAE. The grain is used for FOOD and for ANIMAL FEED. This should not be confused with KAFFIR LIME or with KEFIR milk product.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Any of the covalently closed DNA molecules found in bacteria, many viruses, mitochondria, plastids, and plasmids. Small, polydisperse circular DNA's have also been observed in a number of eukaryotic organisms and are suggested to have homology with chromosomal DNA and the capacity to be inserted into, and excised from, chromosomal DNA. It is a fragment of DNA formed by a process of looping out and deletion, containing a constant region of the mu heavy chain and the 3'-part of the mu switch region. Circular DNA is a normal product of rearrangement among gene segments encoding the variable regions of immunoglobulin light and heavy chains, as well as the T-cell receptor. (Riger et al., Glossary of Genetics, 5th ed & Segen, Dictionary of Modern Medicine, 1992)
Specific regions that are mapped within a GENOME. Genetic loci are usually identified with a shorthand notation that indicates the chromosome number and the position of a specific band along the P or Q arm of the chromosome where they are found. For example the locus 6p21 is found within band 21 of the P-arm of CHROMOSOME 6. Many well known genetic loci are also known by common names that are associated with a genetic function or HEREDITARY DISEASE.
Very long DNA molecules and associated proteins, HISTONES, and non-histone chromosomal proteins (CHROMOSOMAL PROTEINS, NON-HISTONE). Normally 46 chromosomes, including two sex chromosomes are found in the nucleus of human cells. They carry the hereditary information of the individual.
Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
DNA molecules capable of autonomous replication within a host cell and into which other DNA sequences can be inserted and thus amplified. Many are derived from PLASMIDS; BACTERIOPHAGES; or VIRUSES. They are used for transporting foreign genes into recipient cells. Genetic vectors possess a functional replicator site and contain GENETIC MARKERS to facilitate their selective recognition.
Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.
Low-copy (2-50) repetitive DNA elements that are highly homologous and range in size from 1000 to 400,000 base pairs.
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.
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.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.
Complex sets of enzymatic reactions connected to each other via their product and substrate metabolites.
A nucleic acid sequence that contains an above average number of GUANINE and CYTOSINE bases.
Warm-blooded vertebrate animals belonging to the class Mammalia, including all that possess hair and suckle their young.
Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.
The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.
The genetic process of crossbreeding between genetically dissimilar parents to produce a hybrid.
Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
One of the three domains of life (the others being BACTERIA and ARCHAEA), also called Eukarya. These are organisms whose cells are enclosed in membranes and possess a nucleus. They comprise almost all multicellular and many unicellular organisms, and are traditionally divided into groups (sometimes called kingdoms) including ANIMALS; PLANTS; FUNGI; and various algae and other taxa that were previously part of the old kingdom Protista.
One of the three domains of life (the others being BACTERIA and Eukarya), formerly called Archaebacteria under the taxon Bacteria, but now considered separate and distinct. They are characterized by: (1) the presence of characteristic tRNAs and ribosomal RNAs; (2) the absence of peptidoglycan cell walls; (3) the presence of ether-linked lipids built from branched-chain subunits; and (4) their occurrence in unusual habitats. While archaea resemble bacteria in morphology and genomic organization, they resemble eukarya in their method of genomic replication. The domain contains at least four kingdoms: CRENARCHAEOTA; EURYARCHAEOTA; NANOARCHAEOTA; and KORARCHAEOTA.
Genetic loci associated with a QUANTITATIVE TRAIT.
Two identical genes showing the same phenotypic action but localized in different regions of a chromosome or on different chromosomes. (From Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
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.
Deletion of sequences of nucleic acids from the genetic material of an individual.
The outer protein protective shell of a virus, which protects the viral nucleic acid.
A small order of primarily marine fish containing 340 species. Most have a rotund or box-like shape. TETRODOTOXIN is found in their liver and ovaries.
Stretches of genomic DNA that exist in different multiples between individuals. Many copy number variations have been associated with susceptibility or resistance to disease.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.
The chromosomal constitution of cells, in which each type of CHROMOSOME is represented twice. Symbol: 2N or 2X.
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.
Viruses which lack a complete genome so that they cannot completely replicate or cannot form a protein coat. Some are host-dependent defectives, meaning they can replicate only in cell systems which provide the particular genetic function which they lack. Others, called SATELLITE VIRUSES, are able to replicate only when their genetic defect is complemented by a helper virus.
An aberration in which a chromosomal segment is deleted and reinserted in the same place but turned 180 degrees from its original orientation, so that the gene sequence for the segment is reversed with respect to that of the rest of the chromosome.
The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.
Deliberate breeding of two different individuals that results in offspring that carry part of the genetic material of each parent. The parent organisms must be genetically compatible and may be from different varieties or closely related species.
Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.
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.
Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).
The protein complement of an organism coded for by its genome.
Distinct units in some bacterial, bacteriophage or plasmid GENOMES that are types of MOBILE GENETIC ELEMENTS. Encoded in them are a variety of fitness conferring genes, such as VIRULENCE FACTORS (in "pathogenicity islands or islets"), ANTIBIOTIC RESISTANCE genes, or genes required for SYMBIOSIS (in "symbiosis islands or islets"). They range in size from 10 - 500 kilobases, and their GC CONTENT and CODON usage differ from the rest of the genome. They typically contain an INTEGRASE gene, although in some cases this gene has been deleted resulting in "anchored genomic islands".
The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.
Deoxyribonucleic acid that makes up the genetic material of fungi.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The reconstruction of a continuous two-stranded DNA molecule without mismatch from a molecule which contained damaged regions. The major repair mechanisms are excision repair, in which defective regions in one strand are excised and resynthesized using the complementary base pairing information in the intact strand; photoreactivation repair, in which the lethal and mutagenic effects of ultraviolet light are eliminated; and post-replication repair, in which the primary lesions are not repaired, but the gaps in one daughter duplex are filled in by incorporation of portions of the other (undamaged) daughter duplex. Excision repair and post-replication repair are sometimes referred to as "dark repair" because they do not require light.
Diseases of plants.
Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.
A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Chromosomal, biochemical, intracellular, and other methods used in the study of genetics.
The sequence at the 5' end of the messenger RNA that does not code for product. This sequence contains the ribosome binding site and other transcription and translation regulating sequences.
The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.
The material of CHROMOSOMES. It is a complex of DNA; HISTONES; and nonhistone proteins (CHROMOSOMAL PROTEINS, NON-HISTONE) found within the nucleus of a cell.
Deoxyribonucleic acid that makes up the genetic material of algae.
Genes whose nucleotide sequences overlap to some degree. The overlapped sequences may involve structural or regulatory genes of eukaryotic or prokaryotic cells.
Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of MAMMALS.
Retroviruses that have integrated into the germline (PROVIRUSES) that have lost infectious capability but retained the capability to transpose.
An analysis comparing the allele frequencies of all available (or a whole GENOME representative set of) polymorphic markers in unrelated patients with a specific symptom or disease condition, and those of healthy controls to identify markers associated with a specific disease or condition.
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.
A family of BACTERIOPHAGES and ARCHAEAL VIRUSES which are characterized by long, non-contractile tails.
Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.
The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.
Contiguous large-scale (1000-400,000 basepairs) differences in the genomic DNA between individuals, due to SEQUENCE DELETION; SEQUENCE INSERTION; or SEQUENCE INVERSION.

Ribozymes, genomics and therapeutics. (1/9340)

Genome-sequencing projects are proceeding at a rapid pace and determining the function of open reading frames is the next great challenge. Ribozymes with site-specific cleaving activity could aid greatly in this process. High-throughput screening methods to identify optimal target sites for ribozyme cleavage will provide tools for functional genomics as well as therapeutic reagents.  (+info)

Nonmethylated transposable elements and methylated genes in a chordate genome. (2/9340)

The genome of the invertebrate chordate Ciona intestinalis was found to be a stable mosaic of methylated and nonmethylated domains. Multiple copies of an apparently active long terminal repeat retrotransposon and a long interspersed element are nonmethylated and a large fraction of abundant short interspersed elements are also methylation free. Genes, by contrast, are predominantly methylated. These data are incompatible with the genome defense model, which proposes that DNA methylation in animals is primarily targeted to endogenous transposable elements. Cytosine methylation in this urochordate may be preferentially directed to genes.  (+info)

Alternative splicing of transcripts encoding the alpha- and beta-subunits of mouse glucosidase II in T lymphocytes. (3/9340)

Glucosidase II is a processing enzyme of the endoplasmic reticulum that functions to hydrolyze two glucose residues in immature N -linked oligosaccharides attached to newly synthesized polypeptides. We previously reported the cDNA cloning of the alpha- and beta-subunits of mouse glucosidase II from T cells following copurification of these proteins with the highly glycosylated transmembrane protein-tyrosine phosphatase CD45. Subsequent examination of additional cDNA clones, coupled with partial genomic DNA sequencing, has revealed that both subunits are encoded by gene products that undergo alternative splicing in T lymphocytes. The catalytic alpha-subunit possesses two variably expressed segments, box Alpha1, consisting of 22 amino acids located proximal to the amino-terminus, and box Alpha2, composed of 9 amino acids situated between the amino-terminus and the putative catalytic site in the central region of the molecule. Box Beta1, a variably expressed 7 amino acid segment in the beta-subunit of glucosidase II, is located immediately downstream of an acidic stretch near the carboxyl-terminus. Screening of reverse transcribed RNA by polymerase chain reaction confirms the variable inclusion of each of these segments in transcripts obtained from a panel of T-lymphocyte cell lines. Thus, distinct isoforms of glucosidase II exist that may perform specialized functions.  (+info)

An intact sperm nuclear matrix may be necessary for the mouse paternal genome to participate in embryonic development. (4/9340)

We have been interested in determining the minimally required elements in the sperm head that are necessary in order for the paternal genome to participate in embryogenesis. We used an ionic detergent, mixed alkyltrimethylammonium bromide (ATAB), plus dithiothreitol (DTT) to remove the acrosome and almost all of the perinuclear theca, leaving only the sperm nucleus morphologically intact. We also tested the stability of the sperm nuclear matrix by the ability to form nuclear halos. Sperm nuclei washed in freshly prepared 0.5% ATAB + 2 mM DTT completely decondensed when extracted with salt, but nuclei washed in the same buffer that was 1 wk old, and then extracted with salt, produced nuclear halos, indicating stable nuclear matrices. When we treated sperm heads with freshly prepared ATAB+DTT and injected them into oocytes, none of the oocytes developed into live offspring. In contrast, sperm heads treated in the same way but with 1-wk-old ATAB+DTT solution could support development of about 30% of the oocytes to live offspring. Electron microscopy demonstrated that most of the perinuclear theca had been removed in both cases. These data suggest that at least in the mouse, the only component of the spermatozoa that is crucial for participation in embryologic development is the sperm nucleus with a stable nuclear matrix.  (+info)

The prokaryotic beta-recombinase catalyzes site-specific recombination in mammalian cells. (5/9340)

The development of new strategies for the in vivo modification of eukaryotic genomes has become an important objective of current research. Site-specific recombination has proven useful, as it allows controlled manipulation of murine, plant, and yeast genomes. Here we provide the first evidence that the prokaryotic site-specific recombinase (beta-recombinase), which catalyzes only intramolecular recombination, is active in eukaryotic environments. beta-Recombinase, encoded by the beta gene of the Gram-positive broad host range plasmid pSM19035, has been functionally expressed in eukaryotic cell lines, demonstrating high avidity for the nuclear compartment and forming a clear speckled pattern when assayed by indirect immunofluorescence. In simian COS-1 cells, transient beta-recombinase expression promoted deletion of a DNA fragment lying between two directly oriented specific recognition/crossing over sequences (six sites) located as an extrachromosomal DNA substrate. The same result was obtained in a recombination-dependent lacZ activation system tested in a cell line that stably expresses the beta-recombinase protein. In stable NIH/3T3 clones bearing different number of copies of the target sequences integrated at distinct chromosomal locations, transient beta-recombinase expression also promoted deletion of the intervening DNA, independently of the insertion position of the target sequences. The utility of this new recombination tool for the manipulation of eukaryotic genomes, used either alone or in combination with the other recombination systems currently in use, is discussed.  (+info)

Genome reduction in a hemiclonal frog Rana esculenta from radioactively contaminated areas. (6/9340)

A decrease in genome size was found in the hemiclonal hybridogenetic frog Rana esculenta (R. ridibunda x R. lessonae) from areas of radioactive contamination that resulted from the Chernobyl fallout. This genome reduction was of up to 4% and correlated with the background level of gamma-radiation (linear regression corresponded on average to -0.4% per doubling of radiation level). No change in genome size was observed in the coexisting parental species R. lessonae. There was no correlation between genome size and body mass in R. esculenta froglets, which have metamorphosed in the year of the study. The hemiclonal forms may become a suitable object for study on biological significance of individual DNA sequences (and of genome size as a whole) because mutant animals with deletions in a specified genome can arise after a low radiation dose. The proneness to genetic damage makes such forms also a prospective bioindicator of radioactive (and possibly other mutagenic) pollution with the effects of genetic damage conveniently and rapidly monitored by DNA flow cytometry.  (+info)

Sequence analysis of cDNA and genomic DNA, and mRNA expression of the medaka fish homolog of mammalian guanylyl cyclase C. (7/9340)

We isolated the cDNA and genomic DNA encoding a membrane guanylyl cyclase of medaka fish (designated as OlGC6), and determined their complete nucleotide sequences. The open reading frame for OlGC6 cDNA predicted a protein of 1,075 amino acids. Phylogenetic analysis indicated that OlGC6 is a member of the enterotoxin/guanylin receptor family. We also determined the partial genomic structure of the gene of another membrane guanylyl cyclase of medaka fish, OlGC2, which is a member of the natriuretic peptide receptor family. The intron positions relative to the protein-coding sequence are highly conserved in the intracellular domains of OlGC6, OlGC2, mammalian GC-A, and GC-E. Despite their divergent primary structures, some intron positions also seem to be conserved in the extracellular domains of different membrane guanylyl cyclase genes. Northern blot analysis demonstrated that an OlGC6 transcript of 3.9 kb is only present in the intestine, while reverse transcription (RT)-PCR analysis demonstrated that the OlGC6 transcript is present in the kidney, spleen, liver, pancreas, gallbladder, ovary, testis, brain, and eye. RT-PCR also demonstrated that OlGC6 is only expressed zygotically and that transcripts are present from 1 day after fertilization, i.e. long before the intestinal tissues begin to develop.  (+info)

Cloning and characterization of RGS9-2: a striatal-enriched alternatively spliced product of the RGS9 gene. (8/9340)

Regulators of G-protein signaling (RGS) proteins act as GTPase-activating proteins (GAPs) for alpha subunits of heterotrimeric G-proteins. Previous in situ hybridization analysis of mRNAs encoding RGS3-RGS11 revealed region-specific expression patterns in rat brain. RGS9 showed a particularly striking pattern of almost exclusive enrichment in striatum. In a parallel study, RGS9 cDNA, here referred to as RGS9-1, was cloned from retinal cDNA libraries, and the encoded protein was identified as a GAP for transducin (Galphat) in rod outer segments. In the present study we identify a novel splice variant of RGS9, RGS9-2, cloned from a mouse forebrain cDNA library, which encodes a striatal-specific isoform of the protein. RGS9-2 is 191 amino acids longer than the retinal isoform, has a unique 3' untranslated region, and is highly enriched in striatum, with much lower levels seen in other brain regions and no expression detectable in retina. Immunohistochemistry showed that RGS9-2 protein is restricted to striatal neuropil and absent in striatal terminal fields. The functional activity of RGS9-2 is supported by the finding that it, but not RGS9-1, dampens the Gi/o-coupled mu-opioid receptor response in vitro. Characterization of a bacterial artificial chromosome genomic clone of approximately 200 kb indicates that these isoforms represent alternatively spliced mRNAs from a single gene and that the RGS domain, conserved among all known RGS members, is encoded over three distinct exons. The distinct C-terminal domains of RGS9-2 and RGS9-1 presumably contribute to unique regulatory properties in the neural and retinal cells in which these proteins are selectively expressed.  (+info)

Learn all about what the dog genome project is, how it got started and what it can show us. The successful mapping of the dog genome can help in curing both human and canine genetic disorders.
Genome evolution is the process by which a genome changes in structure (sequence) or size over time. The study of genome evolution involves multiple fields such as structural analysis of the genome, the study of genomic parasites, gene and ancient genome duplications, polyploidy, and comparative genomics. Genome evolution is a constantly changing and evolving field due to the steadily growing number of sequenced genomes, both prokaryotic and eukaryotic, available to the scientific community and the public at large. Since the first sequenced genomes became available in the late 1970s, scientists have been using comparative genomics to study the differences and similarities between various genomes. Genome sequencing has progressed over time to include more and more complex genomes including the eventual sequencing of the entire human genome in 2001. By comparing genomes of both close relatives and distant ancestors the stark differences and similarities between species began to emerge as well as ...
The Genome Assembly and Annotation Team carries out genome projects in the classical sense, from design of the de novo sequencing strategy, on through assembly and annotation of the genome.. The team specializes in large eukaryotic genomes and transcriptomes, especially those of animals and plants. Other types of genomes analyzed include those of organelles, endosymbionts, metagenomes and metatranscriptomes, and cancer genomes. Genome assembly is not only difficult due to the sheer size of the data and computational requirements, but also because the biology of genomes is confounded by repetitive elements, polyploidy and variation (single-nucleotide, insertions/deletions, and larger structural variants). The team focuses its efforts on meeting and overcoming these challenges, incorporating new technologies and developing new computational protocols as each project demands.. Annotation of the gene content of the newly assembled genome is key to understanding the genome, once finished. On this ...
DescriptionDe novo Genome assembly and k-mer frequency counting are two of the classical prob- lems of Bioinformatics. k-mer counting helps to identify genomic k-mers from sequenced reads which may then inform read correction or genome assembly. Genome assembly has two major subproblems: contig construction and scaffolding. A contig is a continu- ous sub-sequence of the genome assembled from sequencing reads. Scaffolding attempts to construct a linear sequence of contigs (with possible gaps in between) using paired reads (two reads whose distance on the genome is approximately known). In this the- sis I will present a new computationally efficient tool for identifying frequent k-mers which are more likely to be genomic, and a set of linear inequalities which can improve scaffolding (which is known to be NP-hard) by identifying reliable paired reads. Identifying reliable k-mers from Whole Genome Amplification (WGA) data is more challenging compared to multi-cell data due to the coverage variation ...
SAN DIEGO, Oct. 13, 2016 (GLOBE NEWSWIRE) - BioNano Genomics, the leader in physical genome mapping, together with Howard Hughes Medical Institute (HHMI) Investigator and new Rockefeller University Professor, Erich Jarvis, Ph.D., today announced that his team will use BioNano Genomics Next Generation Mapping (NGM) combined with Pacific Biosciences sequencing technology to construct thousands of vertebrate reference genomes in the Vertebrate Genomes Project.. Dr. Jarviss lab and his collaborator Dr. Olivier Fredrigo, co-director of the Duke University Genome Sequencing Center, performed a systematic evaluation of available DNA sequencing and scaffolding technologies. They concluded that a combination of BioNanos NGM and PacBio sequencing will yield well-structured and informative genome assemblies, making the technologies a very good combination for establishing reference quality genomes.. Dr. Jarvis has purchased an Irys® System for next-generation mapping to play an integral role in ...
A systematic study of genome context methods: calibration, normalization and combination - Background: Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use. Results: We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor. We find that for most organisms the gene neighbor method outperforms the phylogenetic profile method by as much as 40% in sensitivity, being competitive with the gene cluster method at low sensitivities. Gene fusion is generally the worst performing of the
Generation of wt genomes by excision of the BAC vector from the MCMV BAC genome.After transfection of the MCMV BAC plasmid into eukaryotic cells we expected homologous recombination via the duplicated sequences leading to excision of the vector sequences and generation of a wt genome (see Fig. 2 and Fig. 3A, maps 4 and 5). During construction of the original MCMV BAC plasmid pSM3 we had observed that overlength genomes are not stable in cells (22), suggesting that overlength genomes are poorly packaged into viral capsids. Similar observations have been made for other DNA viruses. An overlength of more than 5% over the adenovirus wt genome leads to unstable genomes (2), and Epstein-Barr virus preferentially packages genomes within a very narrow size range (3). Thus, we expected that even when rare recombination events occur at the created target site, preferential packaging of unit length genomes should lead to an accumulation of viruses with the wt genome.. For reconstitution of virus progeny ...
Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence
The mouse genome database (MGD, http://www.informatics.jax.org/), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGDs primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and
In this exercise you will compare the genomes of two Escherichia coli strains, K12 DH10B and B REL606, using whole genome syntenic comparison and high-resolution analyses of specific genomic regions. These analyses will use CoGes tools [[SynMap]] and [[GEvo]] respectively, and will reveal evolutionary changes between these two genomes that happened after the divergence of their lineages. While the nucleotide sequence of these genomes is identical over large expanses of their genomes, many other types of large-scale genomic change will be discovered including phage insertions, transposon transposition, and genomic insertion, deletion, inversion, and duplication events. The computational tools used to do these analyses can be used for comparing genomes of any organisms. First, you are going to identify syntenic regions between these genomes. Syntenic is defined as two or more genomic regions that share a common ancestry and thus are derived from a common ancestor. To do this, you are going to ...
If you have a question about this talk, please contact .. Anthony Doran1, Thomas Keane1,2, and The Mouse Genomes Project consortium 1Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK 2EMBL-EBI, Wellcome Genome Campus, Hinxton, UK. The Mouse Genomes Project has completed the first draft assembled genome sequences and strain specific gene annotation for twelve classical laboratory and four wild-derived inbred mouse strains (WSB/EiJ, CAST /EiJ, PWK /PhJ, and SPRET /EiJ). These strains include all of the founders of the Collaborative Cross and Diversity Outbred Cross. We used a hybrid approach for genome annotation, combining evidence from the mouse reference Gencode annotation and strain-specific RNA -seq and PacBio cDNA, to identify novel strain-specific gene structures and alleles. Approx. 20,000 protein coding genes and 45,000 transcripts are annotated per strain. As these strains are fully inbred, we used heterozygous SNP density as a marker for highly polymorphic loci, and ...
Despite the recent massive progress in production of vertebrate genome sequence data and large-scale efforts to completely annotate the human genome, we still have scant knowledge of the principles that built genomes in evolution, of genome architecture and its functional organization. This work uses bioinformatics and zebrafish transgenesis to explain a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes and to analyze the arrangement of underlying gene regulation systems. Large mammal-teleost conserved chromosomal segments contain highly conserved non-coding elements (HCNEs), their target genes, as well as phylogenetically and functionally unrelated bystander genes. Target genes are developmental and transcriptional regulatory genes with complex, temporally and spatially regulated expression patterns. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are usually expressed in different, less ...
The project was announced on June 11 by MetaMorphix Inc. of Savage, Maryland. The company acquired preliminary (1x) coverage of the cow genome as well as a map of 600,000 cow single nucleotide polymorphisms (SNPs), when it purchased the animal genomics and genotyping business of Celera Genomics of Rockville, Maryland in March. Celera retains a minority business interest in MetaMorphix. Using the preliminary map of likely bovine SNPs, MetaMorphixs genomics division, MMI Genomics in Davis, California, is working with two cattle subsidiaries of the international agribusiness company Cargill to develop a physical map that covers the entire cow genome and also to locate genetic markers associated with cattle traits. Weve taken a different approach than the public projects that are looking into the bovine genome, says Sue Denise, the research and development director of MMI Genomics (formerly the AgGen division of Celera). With this initial sequencing on a substantial amount of the bovine genome, ...
The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. In response, we have developed a suite of quantitative measures to better characterize changes to a genomes annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases - H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. Our results provide the first detailed, historical overview of how these genomes annotations have changed over the years, and demonstrate the usefulness of these measures for genome
Projects Research Projects GEL personnel and collaborators are currently engaged in a variety of research projects Here we focus on describing our research interests and many of the projects described span multiple funding sources The funding section of this site contains more information about the objectives and attribution for individual grants If you don t see what you are looking for here let us know paul genome wisc edu Genome Projects We are engaged in multiple projects aimed at increasing the number and diversity genome sequences from enterobacteria These include plant pathogenic enterobacteria which remain underrepresented among complete genomes available as well as neglected genera isolated from a wide variety of sources Software and Database Development We have built several tools to assist with annotation and comparative analysis of genome data These include Mauve a widely used multiple genome aligner and the ASAP database The Software section of this web site includes additional ...
I thought you might be interested in looking at dog genome.. http://www.bordercollie.org/boards/topic/8688-dog-genome/?do=findComment&comment=97997 ...
Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and Chromosome Conformation Capture methods, the availability of experimental data on genome three-dimensional (3D) organization has dramatically increased. We now have access to unprecedented details on how genomes organize within the interphase nucleus. Development of new computational approaches that leverage such data has already resulted in the first 3D structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. 3D Genomes proposes to continue developing computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. Then, such methods will be applied to address outstanding questions in genome biology, which shall provide insight into the ...
Abstract: The current status of the functional annotations associated with the human genome is in a rudimentary state. The majority of current genome annotations is heavily protein coding gene centric. This focus on protein coding genes intrinsically influences current perceptions of how the genome is structured and is regulated. This view of the genome also has an underlying supposition that transcripts with very little coding potential are not biologically important. However, recent unbiased experiments analyzing the sites of transcription across large sections of the human genome have led to the conclusion that the current human genome annotations can not account for the amounts of empirically detected transcription. (Kapranov, et al. 2002; Rinn, et al., 2003, Kampa, et al., 2004, Martone, et al., 2003, Cawley et al., 2004). Most of the detected unannotated transcription is composed of RNAs with very little coding capacity (,100 aa). These transcripts of unknown function (TUFs) share many ...
2017-02-16 15:06:47] Checking for Bowtie Bowtie version: 2.2.8.0 [2017-02-16 15:06:47] Checking for Bowtie index files (genome).. [2017-02-16 15:06:47] Checking for reference FASTA file [2017-02-16 15:06:47] Generating SAM header for genome [2017-02-16 15:06:47] Preparing reads left reads: min. length=75, max. length=75, 100 kept reads (0 discarded) right reads: min. length=75, max. length=75, 100 kept reads (0 discarded) [2017-02-16 15:06:47] Mapping left_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping left_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg2 to genome genome with Bowtie2 (2/3) [2017-02-16 15:06:47] Mapping left_kept_reads_seg3 to genome genome with Bowtie2 (3/3) [2017-02-16 15:06:47] Mapping right_kept_reads to genome genome with Bowtie2 [2017-02-16 15:06:47] Mapping right_kept_reads_seg1 to genome genome with Bowtie2 (1/3) [2017-02-16 15:06:48] Mapping right_kept_reads_seg2 to genome genome with Bowtie2 ...
We first determined whether genome build information is consistently supplied along with submissions to public repositories. As a representative example, we examined the records in the GEO and ENCODE databases with the following search criteria. In the GEO database, we examined all the records (one sample per series) that involved high-throughput sequencing submitted after 31 December 2008 for three species: Homo sapiens; Mus musculus; and Drosophila melanogaster. We then checked whether the data-processing section of metadata explicitly mentioned the genome build information, by case-insensitively searching for the following words: {hg17,hg18,hg19,hg38,grch36,grch37,grch38,build37.2,build37.1,build36.3,ncbi35,ncbi36,ncbi37,mm8,mm9,mm10,grcm38,bdgp6,bdgp5,bdgp5.25,build5.41,build5.3,build5,build4.1,dm6,dm3,ncbi}. In the ENCODE database, we examined the metadata file of all records.. Around 23.0% of the queried series records did not contain the genome build information explicitly in the ...
Links to domain combinations containing the Oncogene products superfamily in all genomes. Links for both groups of genomes, such as eukaryotes, bacteria and archaea, and individual genomes are provided.
Im looking to have a single FASTA sequence for each chromosome in an organism, but if I check the sequences in panTro5.fa (chimp) that Ive downloaded from UCSC I get a ton of ids like: chr10_NW_015973889v1_random, chr10_NW_015973890v1_random, etc.. What are these and how do I get rid of them? I dont have them in my hg38.fa (human) file because you can download all the chromosomes individually and then assemble them into one fasta, but I dont think you get that option with other genomes.. I need to use the genomes to find hits for viral LTR sequences and the number of hits is important so I dont want to get the same hit in the same region of the genome twice or more.. ...
Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular. We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, which models possibly duplicated
1. Clicking on View Rat Genes Report (3 in RGD Search Result above) provides a list of gene records containing the search term (bold).. 2. The list is tabbed for each species and is exportable (see below).. 3. Descriptive information is presented in columns - the gene symbol links to the gene report page.. 4. Search results can be filtered by genome assembly or by chromosome, and it is sortable by any column heading. Additional searches for the specific data object and species can be performed from this page by entering a different or additional term in the Refine Term box and clicking Update. Search results for other objects such as QTLs and strains, are configured similarly.. ...
Background: Recovering the structure of ancestral genomes can be formalized in terms of properties of binary matrices such as the Consecutive-Ones Property (C1P). The Linearization Problem asks to extract, from a given binary matrix, a maximum weight subset of rows that satisfies such a property. This problem is in general intractable, and in particular if the ancestral genome is expected to contain only linear chromosomes or a unique circular chromosome. In the present work, we consider a relaxation of this problem, which allows ancestral genomes that can contain several chromosomes, each either linear or circular. Result: We show that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem. This result holds in the more general case where columns have bounded multiplicity, ...
View Notes - Lecture 2 from PLB 40175 at UC Davis. PLB 113 Lecture 2 II. Genome Organization and Gene Expression A. Plants have big (and small genomes) B. Genomes consist of single (LOW) copy and
The NIH is now accepting applications for the Somatic Cell Genome Editing (SCGE) program. The SCGE program aims to improve genome editing technologies to accelerate the translation of this technology into clinical applications and maximize the potential to treat as many diseases as possible. Pending the availability of funds and sufficient numbers of meritorious applications, the NIH expects to fund projects to provide better animal models for assessing genome editing in vivo, tools and assays to detect adverse consequences of genome editing in human cells, new technologies to deliver genome editing machinery into disease relevant cells and tissues in vivo, novel genome editing and engineering systems, and a Dissemination and Coordinating Center. Applications are due April 3, 2018. For additional information on these RFAs visit our Funding Opportunities page.. ...
Curated databases of completely sequenced genomes have been designed independently at the NCBI (RefSeq) and EBI (Genome Reviews) to cope with non-standard annotation found in the version of the sequenced genome that has been published by databanks GenBank/EMBL/DDBJ. These curation attempts were expected to review the annotations and to improve their pertinence when using them to annotate newly released genome sequences by homology to previously annotated genomes. However, we observed that such an uncoordinated effort has two unwanted consequences. First, it is not trivial to map the protein identifiers of the same sequence in both databases. Secondly, the two reannotated versions of the same genome differ at the level of their structural annotation. Here, we propose CorBank, a program devised to provide cross-referencing protein identifiers no matter what the level of identity is found between their matching sequences. Approximately 98% of the 1,983,258 amino acid sequences are matching, allowing
The Mouse the premier animal model for studying human disease the premier animal model for studying human disease > 95% same genes > 95% same genes same diseases, similar reasons (e.g., cancer, hypertension, diabetes, osteoporosis, …) same diseases, similar reasons (e.g., cancer, hypertension, diabetes, osteoporosis, …) 1000s lab strains, diff. characteristics 1000s lab strains, diff. characteristics precise genetic control precise genetic control
Nobody mentioned junk DNA and the resolution of the C-value paradox. Nobody mentioned the small number of genes in the human genome in spite of the fact that a great many articles begin with the claim that this was a shocking discovery [but see False History and the Number of Genes]. Jernej Ule mentioned alternative splicing but nobody else did in spite of the fact that many papers claim that most human genes are capable of making several different proteins. This is also a false claim, IMHO, but youd never know that from reading the journal. Peter Fraser was the only one who mentioned the vast regulatory network of enhancers as claimed by the ENCODE Consortium. If true, that would clearly count as a major discovery. (Its not true.) Eukaryotic genomes are chock full of defective transposons but none of the editors thought that was a key advance in our understanding of the genome ...
The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here we review the main computational pipelines used to generate the human reference protein-coding gene sets.
Symbol: This is the official symbol assigned to this strain according to the strain nomenclature guidelines. This is a combination of strain and substrain designations for inbred strains (or symbol and ILAR code for other strain types).. Strain: The official strain symbol.. Substrain: The official substrain symbol - this can be a collection of ILAR lab codes defining the history of this particular strain. Can also be found in pulldown section below with links to the strain report pages.. Full Name: If the strain has a text name then it is displayed here; this is not visible if no name is associated to the strain, as in this example. Ontology ID: The identification number of the strain ontology term assigned by RGD, linked to the term in the ontology browser. In the strain ontology, rat strains are organized in a hierarchical fashion based on the type of strain and the way they were developed.. Also known as: Old symbols and synonyms that were used for the strain. If a strain is renamed to comply ...
by vulgavis , Jun 16, 2020 , Biology, Genome Biology, Mobile DNA, Nature Communications, Scientific Reports, TE Day, Technology, TEs, transposable elements, Transposons , 0 , ...
The Department of Genetics and Genome Biology at the University of Leicester occupies a recently-refurbished, modern, purpose-built laboratory space, furnished with up-to-date equipment for the latest molecular genetic methods. We have an array of facilities both in-department and within the College of Life Sciences.
Comparative assembly using multiple genomes.The target genome is shown in the center, aligned to two related genomes, A and B. The DNA sequence of the target di
Highly fragmented reference genomes (with thousands or more short contigs or scaffolds) have been a persistent challenge for our small RNA-seq analysis program ShortStack. During a run, ShortStack needs to retrieve genomic sub-sequences for analysis of predicted RNA secondary structure. This is required to identify MIRNA hairpins. Early on I made the decision to use the samtools faidx function as the engine to retrieve genome sub-sequences. This was just pragmatic and lazy .. samtools was already required for other portions of ShortStacks analysis, and there wasnt a need to reinvent the wheel. However, when we started to do runs against highly fragmented genome assemblies, we found analysis was very slow. The slowness was traced to the samtools faidx function, which is very sensitive to the number of contigs/references.. The first attempt to fix this issue was in version 3.0, when I introduced the use genome-stitching. When the reference genome had more than 50 sequences, and some were , 1Mb ...
ENCODES a protein that exhibits transcription factor binding (ortholog); INVOLVED IN cell growth involved in cardiac muscle cell development (ortholog); cellular response to growth factor stimulus (ortholog); cellular response to hypoxia (ortholog); PARTICIPATES IN platelet-derived growth factor signaling pathway; ASSOCIATED WITH atrial fibrillation (ortholog); Cardiomegaly (ortholog); congenital megabladder (ortholog); FOUND IN nucleus (ortholog)
Two scientists claim to have pushed the boundaries of what can be learned about the ancestral history of the human race from one persons genome. Dr Richard Durbin and Dr Heng Li from the UKs Wellcome Trust Sanger Institute in Cambridge used information from the genomes of only seven people to show that humans living in Europe and China endured a severe population bottleneck between 10,000 and 60,000 years ago.. In the study published in Nature, the scientists used a new statistical technique to analyse differences between alleles within a genome. They found the more similar the alleles, the more recent the genetic separation was between parents - and by calculating the separation date, the researchers were able to estimate past population sizes. Each human genome contains information from the mother and the father, and the differences between these at any place in the genome carry information about its history, Dr Li said.. Scientists have traditionally performed this kind of analysis on ...
Institutions: The Jackson Laboratory. The release of the publicly accessible mouse genome sequence for the C57BL/6J strain of the laboratory mouse represents a landmark event in genome biology. The ability of researchers to use the mouse genome sequence effectively will depend, in large part, on how well the genes and other features identified in the sequence are integrated with the biological data sets available for the mouse that are available from the Mouse Genome Informatics (MGI) database. Model organism databases, such as MGI, have a unique role to play in connecting sequence and biology and in curating these connections for the long term.. The ways in which sequence data are stored and subsequently accessed from MGI are changing rapidly. Results of these significant enhancements to the capacity of the database will better enable the mouse genetics and genomics research communities to find biological meaning in the mouse genome sequence. I will present the status of our sequence-to-biology ...
Lasergene Genomics allows you to quickly and easily perform and edit de novo genome assemblies from any sequencing platform. Click here to find out more!
With an increasing amount of whole genome sequence data becoming available on a daily basis we have an opportunity to study the interactions and dynamics of different organisms on a whole genome level. In the past, reports of horizontal gene transfer have focused mainly on the identification of single genes that show distorted phylogenetic profiles to that of the organism it was isolated from. This study firstly did whole genome comparisons between the rice nuclear and plastid genomes to determine the level and dynamics gene transfer and insertion of the chloroplast ad mitochondrial genomes into that of the nuclear genome of rice. Secondly, it looked to identify sequence similarities between the rice genome and microbial genomes by performing whole genome comparisons between the rice genome and that of several microbial genomes. These sequences were analyzed further to identify possible instances of horizontal transfer of DNA from microbes to the rice genome. Using this approach, this study ...
The genomic sequences of many important Triticeae crop species are hard to assemble and analyse due to their large genome sizes, (in part) polyploid genomes and high repeat content. Recently, the draft genomes of barley and bread wheat were reported thanks to cost-efficient and fast NGS technologies. The genome of barley is estimated to be 5 Gb in size whereas the genome of bread wheat accounts for 17 Gb and harbours an allo-hexaploid genome. Direct assembly of the sequence reads and access to the gene content is hampered by the repeat content. As a consequence, novel strategies and data analysis concepts had to be developed to provide much-needed whole genome sequence surveys and access to the gene repertoires. Here we describe some analytical strategies that now enable structuring of massive NGS data generated and pave the way towards structured and ordered sequence data and gene order. Specifically we report on the GenomeZipper, a synteny driven approach to order and structure NGS survey sequences of
We anticipate that the cannabis genome and transcriptome sequences will be invaluable for understanding the unique biological properties and considerable phenotypic variation in the genus Cannabis. These genomic resources are applicable to the molecular analysis of both marijuana and hemp, as we sequenced a marijuana strain (PK) and two hemp cultivars (Finola and USO-31) grown in Canada and elsewhere. The high repeat content of plant genomes, coupled with the relatively high level of sequence variation in cannabis [47-49], complicates the assembly of the full genome into the anticipated nine autosomes and two sex chromosomes. We will continue to explore approaches that might facilitate assembly of the full genome sequence, including anchoring the genome using molecular markers or FISH (fluorescence in situ hybridization) [50]. A more complete assembly might provide the sequences of the × and Y chromosomes and help shed light on the mechanism of sex determination in cannabis. Nonetheless, ...
Background: Geminivirus (family Geminiviridae) is a prevalent plant virus that imperils agriculture globally, causing serious damage to the livelihood of farmers, particularly in developing countries. The virus evolves rapidly, attributing to its single-stranded genome propensity, resulting in worldwide circulation of diverse and viable genomes. Genomics is a prominent approach taken by researchers in elucidating the infectious mechanism of the virus. Currently, NCBI Viral Genome website is a popular repository of viral genomes that conveniently provides researchers a centralized data source of genomic information. However, unlike the genome of living organisms, viral genomes most often maintain peculiar characteristics that fit into no single genome architecture. By imposing a unified annotation scheme on the myriad of viral genomes may downplay their hallmark features. For example, virion of Begomovirus prevailing in America encapsulates two similar-sized circular genomes and both are required to
Multiple laboratories now offer clinical whole genome sequencing (WGS). We anticipate WGS becoming routinely used in research and clinical practice. Many institutions are exploring how best to educate geneticists and other professionals about WGS. Providing students in WGS courses with the option to analyze their own genome sequence is one strategy that might enhance students engagement and motivation to learn about personal genomics. However, if this option is presented to students, it is vital they make informed decisions, do not feel pressured into analyzing their own genomes by their course directors or peers, and feel free to analyze a third-party genome if they prefer. We therefore developed a 26-hour introductory genomics course in part to help students make informed decisions about whether to receive personal WGS data in a subsequent advanced genomics course. In the advanced course, they had the option to receive their own personal genome data, or an anonymous genome, at no financial cost to
There are several more eukaryotic genome sequences on the way: mouse, Fugu, zebrafish, rat, rice, dog and more, with further announcements of genome projects likely in the next few years as the genome centers start to look for new projects. Richard Mural (Celera Genomics Inc.) described the 5.5x whole-genome shotgun coverage of the mouse genome generated by Celera http://www.celera.com/. Using three strains of laboratory mouse (129X1/SvJ, A/J, and DBA/2), Celera have identified 2.7 million SNPs where sequence derived from separate strains overlaps and contains discrepancies. Mural also reported the amazingly high rate of SNPs found within strains, one in 10,000 nucleotides across the genome, although under cross-examination by Eric Lander (Whitehead Institute, Cambridge, USA), Mural admitted that many of these SNPs probably reflect sequencing errors.. As expected, Celera have been finding good correlation of synteny between the mouse and human genomes. An interesting general theme emerging from ...
New release of WormBase WS223, Wormpep223 and Wormrna223 Mon Jan 24 12:12:08 GMT 2011 WS223 was built by Paul Davis -===================================================================================- The WS223 build directory includes: genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data genomes/b_malayi: - genome_feature_tables/ sequences/ genomes/c_brenneri: - genome_feature_tables/ sequences/ genomes/c_briggsae: - genome_feature_tables/ sequences/ genomes/c_elegans: - annotation/ genome_feature_tables/ sequences/ genomes/c_japonica: - genome_feature_tables/ sequences/ genomes/c_remanei: - genome_feature_tables/ sequences/ genomes/h_bacteriophora: - genome_feature_tables/ sequences/ genomes/h_contortus: - genome_feature_tables/ sequences/ genomes/m_hapla: - genome_feature_tables/ sequences/ genomes/m_incognita: - sequences/ genomes/p_pacificus: - genome_feature_tables/ sequences/ *annotation/ - contains additional annotations i) confirmed_genes.WS223.gz ...
It turns out that sequencing individual genomes in a population reveals a rich tapestry of variation that is lost when analyzing the average of DNA pooled from larger cell numbers. Kun Zhang, Mike McConnell and Xuyu Cai (Christopher Walsh lab) have been applying single-cell genome sequencing to neuronal cells, finding that a subset of cells can often harbor mutations not seen elsewhere in the brain, creating a patchwork of genotypes. The Single Cell Analyses meeting took place at the same time as The Scripps Institutes Future of Genomic Medicine conference, which focuses on the field of personal genomes. The mosaicism revealed by single-cell genome sequencing serves as an important reminder that each person has not one personal genome, but many.. Perhaps the best known application of single-cell genome sequencing is the tracking of tumor evolution, where the power of single-cell analyses is leveraged against the known genomic instability, and hence within-individual variability, of cancer ...
On July 8th-9th 2016 scientists from around the world will convene in Edinburgh at Dynamic Earth to discuss the progress of the international synthetic yeast genome project as well as other advances in genome engineering including genome assembly methodologies, mammalian synthetic biology, lab automation and software development for synthetic biology (for more details, go to conference website: http://syngenomesconf.cailab.org).. For the past four years, the conference has focused on the ongoing Synthetic Yeast Genome Project (Sc2.0). As the worlds first synthetic, designer eukaryotic genome project, the Synthetic Yeast Genome Project has garnered global attention. The Sc2.0 international consortium is building 16 designer synthetic chromosomes encompassing ~12 million base pairs of DNA, and we are around halfway through this very exciting project.. The conference has been expanded to include a focus on Synthetic Genomes and Engineering Biology. This is a hot topic and we are thrilled to ...
Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the
To construct a new genome assembly we utilized all existing genomic data generated from Cinnamon, a female Abyssinian cat used for all prior genome assemblies (Pontius et al. 2007; Montague et al. 2014), with the exception of felCat4 (Mullikin et al. 2010), which also included reads from multiple breeds and a wild cat (Felis silvestris lybica). The data from prior maps included ∼2 × whole genome coverage of Sanger-based sequencing (6.7 million plasmid and 1.3 million 40 kb fosmid end reads; Pontius et al. 2007), ∼12 × whole genome coverage with 454 sequencing (6 × fragment and 6 × of 3 kb paired-end reads), and Sanger-based end-sequenced BACs (Amplicon Express Felis catus FSCC library) (Montague et al. 2014). Here, we generated ∼20 × coverage of nonoverlapping 100 bp paired-end reads from a single Illumina short-insert (avg. length = 350 bp) library, prepared from Cinnamons DNA, on the HiSeq2000 (SRA Accession numbers SRX478589 and SRX478590). The new Illumina reads were combined ...
In order to contribute to the establishment of a complete map of transcribed regions of the human genome, we constructed a testicular cDNA library for the cynomolgus monkey, and attempted to find novel transcripts for identification of their human homologues. The full-insert sequences of 512 cDNA clones were determined. Ultimately we found 302 non-redundant cDNAs carrying open reading frames of 300 bp-length or longer. Among them, 89 cDNAs were found not to be annotated previously in the Ensembl human database. After searching against the Ensembl mouse database, we also found 69 putative coding sequences have no homologous cDNAs in the annotated human and mouse genome sequences in Ensembl. We subsequently designed a DNA microarray including 396 non-redundant cDNAs (with and without open reading frames) to examine the expression of the full-sequenced genes. With the testicular probe and a mixture of probes of 10 other tissues, 316 of 332 effective spots showed intense hybridized signals and 75 cDNAs were
During sequencing, its possible to specify the variety of base pairs that are read at a moment. Since mobile components are eliminated from eukaryotic genomes so slowly, theyve accumulated to the point at which they now constitute an important section of the genomes of many eukaryotes. buy essay online Theres no correlation between the range of genes and its complexity.. The HMM includes eight or nine homozygous genotype states, based on the amount of founders that contributed to every line. Other genomes are sequenced with the exact same intention of aiding conservation-guided techniques, for exampled the pufferfish genome. They are essential to genetic research.. The majority of these mutations are single nucleotide changes in noncoding parts of the genome and will most likely have minimum functional significance. https://pasadena.edu/campus-life/student-gov-clubs.php This method is apparently dominated by genetic drift caused by small population size, very low recombination prices, and ...
The genome of a female Hereford cow has been sequenced by the Bovine Genome Sequencing and Analysis Consortium, a team of researchers led by the National Institutes of Health and the U.S. Department of Agriculture.[1] It is one of the largest genomes ever sequenced. The results, published in the journal Science on April 24, 2009,[2] are likely to have a major impact on livestock breeding.[3] They were obtained by more than 300 scientists in 25 countries after six years of effort.. The size of the bovine genome is 3 Gb (3 billion base pairs). It contains approximately 22,000 genes of which 14,000 are common to all mammalian species. Bovines share 80 percent of their genes with humans; cows are less similar to humans than rodents (humans and rodents belong to the clade of Supraprimates). They also have about 1,000 genes shared with dogs and rodents but not identified in humans.[4]. The charting of key DNA differences, also known as haplotypes, between several varieties of cattle could allow ...
The grapevine is the fourth flowering plant whose genome sequence has been made public by a French-Italian public consortium that carried out the Whole Genome Shotgun 8X sequence of a quasi-homozygous genotype, PN40024. Recently the 12X version of the genome was completed. All data were generated by paired-end sequencing plasmid, fosmid and BAC libraries of different insert sizes, using Sanger technology. Using 11.91X coverage, an assembly of 499 Mb was obtained, composed of 2,888 super-contigs, 91% of which are anchored on linkage groups. The automatic annotation led to an estimate of 26,347 protein coding gene models. The grape genome was shaped by two ancient whole genome duplications that were not followed by extensive rearrangements, thus enabling the discovery of ancestral traits and features of the genetic organization of flowering plants. This sequence allows now to set up powerful integrative approaches for the identification of key genes for important traits in grapevine, to have a ...
Where did this copy of AS originate from? It aligned well with the version of AS from P. aeruginosa and appeared to have a bacterial origin but was not found on the C. ruddii genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of C. ruddii the source of this sequence appeared to be the nuclear genome of P. venusta itself. The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that C. ruddii has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count. ...
The UMD 3.1 assembly (NCBI assembly accesion GCA_000003055.3), released in December 2009, is the third release of the cow (Bos taurus) assembly from the Center for Bioinformatics and Computational Biology (CBCB) at University of Maryland. The genome sequences were generated using a combination of BAC-by-BAC hierarchical (~11 million reads) and whole-genome shotgun (~24 million reads) sequencing methods, assembled using the Celera Assembler version 5.2. The total length of the UMD3.1 assembly is 2.65Gb. The N50 size is the median sequence length, i.e. 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size for contigs in the UMD3.1 assembly is 103785. The genome assembly represented here corresponds to GenBank Assembly ID GCA_000003055.3. ...
This is the website for the Reed Labs Butterfly Genome Database at Cornell University.. This site provides a portal for searching and browsing high quality butterfly genome assemblies that are annotated with specialized data types including gene expression (e.g. RNA-seq), chromatin structure, and SNP variation. Data will be added on a rolling basis, and we encourage contributions from other research groups.. Blast: Search genome assemblies and gene predictions using Blast. Genome browser links are embedded in Blast result for your convenience.. Genome Browser: We use the UCSC genome browser as the most powerful current interface for manipulating and viewing complex data tracks. On this page you can go directly to any relevant coordinate in any genome we host.. Downloads: Download genome assemblies and accessory data tracks, as well as custom scripts from Reed Lab publications.. Citations: Publications to cite for specific data sets.. Please note that there are many additional lepidopteran ...
To whom it may concern: The completion of the sequencing of the entire DNA of the S. cerevisae genome, is a major event in the history of biology. All those involved are to be congratulated as we now have the first full genetic blueprint of a free living eukaryotic organism. The analysis of these gene products will provide us with a powerful tool for reading the genomes of other eukaryotes, particularly those of higher eukaryotes, which represent the majority of the data currently in the genetic databases. The analysis of the yeast genome is provided a useful framework for the annotation of many of the complete genome projects currently nearing completion, as well as the upcoming human genome. The yeast sequence information used to create this yeast webpage was provided by the GeneQuiz Consortium and the Mips Genome Commission . We have made an initial attempt to integrate these two data structures as well as supplement their annotation with that obtained ,From a set of functionally diagnostic ...
The genes within the genome (genetic code) of cattle need to be identified and defined before variability of these genes among cattle (individuals and breeds) can be identified. One goal is to determine whether such variations when found are associated with enhanced or decreased resistance to infectious diseases. The cattle genome has been largely sequenced (that is, the genetic code read), and now one of the purposes of the international community effort is to annotate the bovine genome (define genes within the genetic code).
Common plasmids are simple DNA molecules which contain a few genes and regulatory elements. Most viral genomes are more complex. For example, the genome of phage lambda contains approximately 50 genes. About 4,000 genes are present in the E. coli genome while there is approximately 1,000 times more DNA in the genome of a mammal. This progression in genome complexity is the topic of this exercise. Here, students compare the electrophoretic patterns of restriction digests of a plasmid, phage lambda DNA, and cow DNA from thymus and kidney as shown in the figure below. The exercise serves as a good introduction for determining the size of DNA molecules and provides an appreciation for the complexity of genomes from different organisms.. ...
Putting the Genome on the Map. The scale of the human genome is staggering. Our 80,000 genes account for only a small part of the delicate thread of three thousand million bases of sequence that we carry on our chromosomes. Encoded within this part of the sequence are the Instructions for making a complete set of proteins that drive all of the processes in our cells. We have almost no idea about what functions, if any, the rest of the sequence might have. Determining the sequence of the human genome - both that of the genes and that of the non-coding regions - is going to tell us much about our biology. However, there is also a lot that we will not be able to fathom from the sequence of the human genome alone. We need to broaden our horizons when thinking about the map of the human genome and the richness of information that we want it to contain. We need to understand how chromosome environment can perturb gene function every bit as effectively as mutation within gene sequence and how ...
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point
Links to domain combinations containing the Amb V allergen superfamily in all genomes. Links for both groups of genomes, such as eukaryotes, bacteria and archaea, and individual genomes are provided.
Health, ... Genome Research ( www.genome.org...Included in this special issue are novel biological insights gained fr...1. Whole-genome and whole-exome sequencing: Searching for the drivers...Cancer is believed to arise through the accumulation of genetic and ep...,Genome,Research,publishes,special,issue:,Cancer,Genomics,medicine,medical news today,latest medical news,medical newsletters,current medical news,latest medicine news
An approximation to the ~4-Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ~90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single bp mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome-pairs have one or two recombinant transfers of length ~40-115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. ...
Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data. However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. We present here the RepetDB database developed
The primary mission of the Alliance of Genome Resources (the Alliance) is to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease. This understanding is fundamental for advancing genome biology research and for translating human genome data into clinical utility.
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldnt know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldnt be in their genome. Sponges dont have a nervous system, yet they have many of the ...
If LUA had a simple genome (like a simple bacterium) and genetic complexity and all the additional information accumulated over the course of evolution, we should be able to trace this accumulation by examining the genomes of different organisms on different levels of complexity. This is a reasonable expectation. (If we wouldnt know about the c-value paradox or about the recent results of actual DNA sequences, one should reasonably expect to see this accumulation, given the Darwinian framework. ) A compelling starting point could be the genome of a sponge. This creature is one of the most simple multicellular organisms. However, the content of the genome of Amphimedon queenslandica - a marine sponge - literally shocked the scientific community.4 This simple creature has a remarkably complex genome with more individual genes than an average bird, but the most stunning part is that they posses genes that shouldnt be in their genome. Sponges dont have a nervous system, yet they have many of the ...
Models were annotated by projecting transcripts annotated by Ensembl from a reference genome, through a BLASTZ DNA alignment of this genome to a reference genome ...
Models were annotated by projecting transcripts annotated by Ensembl from a reference genome, through a BLASTZ DNA alignment of this genome to a reference genome ...
A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called enhancer sequences.1 These are novel DNA features that were once thought to be a part of the so-called junk DNA regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.. The new technology described in this report is called STARR-seq, or self-transcribing active regulatory region sequencing. This new technique allows for the more effective identification and characterization of enhancer sequences, which help recruit proteins called transcription factors that regulate gene activity. Enhancers are found in the non-protein coding regions of the genome both within and surrounding genes. In the past, enhancers have been difficult to characterize accurately.. This new study adds yet another layer of deduced complexity in the ...
A new type of DNA sequencing technology has been developed and used to identify and characterize key regions of the genome called enhancer sequences.1 These are novel DNA features that were once thought to be a part of the so-called junk DNA regions of the genome. These key elements are now proven to be part of the indispensable and irreducibly complex design inherent to proper gene function for all types and categories of genes.. The new technology described in this report is called STARR-seq, or self-transcribing active regulatory region sequencing. This new technique allows for the more effective identification and characterization of enhancer sequences, which help recruit proteins called transcription factors that regulate gene activity. Enhancers are found in the non-protein coding regions of the genome both within and surrounding genes. In the past, enhancers have been difficult to characterize accurately.. This new study adds yet another layer of deduced complexity in the ...
The above wasnt a population genomic paper. They didnt have large sample sizes, nor were they focusing on questions that applied to the microevolutionary scale (within species level lineages). Rather, they were comparing the genomes of Caenorhabditis lineages which diverged on the order of ~30 million years ago. The effective population size difference between selfing and outcrossing lineages is huge, with the authors reporting N e , 10,000 for C. elegans N e , 1,000,000 for C. remanei. This is a big deal because variation in effective population size has been argued by many, foremost Mike Lynch, as one of the drivers of the phenomenon of huge genome size differences. Lynch is a fertile mind with many ideas, and if you are curious about them Id recommend a purchase and read through of The Origins of Genome Architecture. But the upshot from this paper seems to be that the broader thesis of Lynch and his supporters is not favored by these specific results utilizing comparative genomics. Every ...
In Genome Biology this week: genomic sequencing of milkweed bug, benchmark comparison of single-cell RNA sequencing platforms, and more.
The D. subobscura genome has been used to track global climate change by measuring the magnitude and direction of shifts in ... The genome of some Greek populations of D. subobscura has shown evidence of microgeographic variation, prompting a possibility ... Additionally, the genome does not show a chromocenter and contains high levels of chromosomal polymorphisms caused by ... As of March 2019, the first long-read sequencing of D. subobscura's genome has been presented, showing that evolution of its ...
In the specific differentiation, C. rhomboideum likely underwent genome size reduction. Approximately 5% of the genome is ... The genome of C. rhomboideum is smaller than that of C. annuum. ...
A separate study by Wilson and Strobeck, published in Genome, was done to define the relationships between different herds of ...
Genome. 49 (8): 873-881. doi:10.1139/g06-043. ISSN 0831-2796. PMID 17036061. Tsurushima, Tetsu; Don, L. Dinh; Kawashima, Kenji ...
24, June 13, 1919, p. 29 "Ivanhoe". Genome. BBC. Retrieved 4 April 2020. Dailey MacKinlay, M. Sterling. Garcia the Centenarian ...
Genome. 10 (5): 506-12. doi:10.1007/s003359901031. PMID 10337626. NCBI. "Homo sapiens COX4 neighbor (COX4NB), transcript ...
Schmutz SM, Moker JS (1991). "A cytogenetic comparison of some North American owl species". Genome. 34 (5): 714-717. doi: ...
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Genome. 55 (5): 396-399. doi:10.1139/G2012-022. PMID 22533489.. ...
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For example, an LJJ individual would be a triploid with one A. laterale genome and two A. jeffersonianum genomes, while an ... This is in contrast to hybridogenesis, where the maternal genomes are passed hemiclonally and the paternal genome is discarded ... Sperm incorporation commonly takes the form of genome addition (resulting in ploidy elevation in the offspring), or genome ... The offspring of a single mother may have different genome complements; for example, a single egg mass may have both LLJJ and ...
Genome. Retrieved 4 December 2020. "Radio Times, Issue 312, Southern, 22 September 1929 - 28 September 1929". Genome. Retrieved ...
Genome. 16 (12): 942-54. doi:10.1007/s00335-005-0075-2. PMID 16341674. S2CID 69278. Ramachandran P, Boontheung P, Xie Y, et al ... Bonaldo MF, Lennon G, Soares MB (1997). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome ...
Gladfelter, A.; Berman, J. (2009). "Dancing genomes: fungal nuclear positioning". Nature Reviews Microbiology. 7 (875-886): 875 ... ISBN 978-0306472619 Mortimer, Robert K.; Romano, Patrizia; Suzzi, Giovanna; Polsinelli, Mario (December 1994). "Genome renewal ... "genome renewal" and provides an advantage of sex that does not depend on outcrossing. Candida albicans is a diploid fungus that ... Genome. 35 (5): 815-26. doi:10.1139/g92-124. PMID 1427061. Herskowitz I (December 1988). "Life cycle of the budding yeast ...
But... You won't be using me anymore... Battle data... from the Perfect Soldier? Genes... genome... I see... Intriguing... I'll ...
... implications for taxonomy and biogeographic origins from whole-genome data sets" (PDF). Genome. 49 (9): 1115-1130. doi:10.1139/ ...
Aegilops (genome) Comparative Classification Table Triticum (genome) Comparative Classification Table Genomes in Aegilops, ... speltoides - ancient food grain, putative source of B genome in bread wheat[clarification needed] and G genome in T. ... produces the genome StSt and another Hordeum then genome = HH. Allotetraploid combinations of Pseudoroegeneria and Hordeum and ... A Genome) timopheevii (Sanduri wheat) turgidum (poulard wheat) (AABB Genome) carthlicum (Persian black wheat) dicoccoides (wild ...
CS1 maint: discouraged parameter (link) "Wildlife on One: Meerkats Divided". Genome. Retrieved 16 August 2019. CS1 maint: ...
Horvath S (2013). "DNA methylation age of human tissues and cell types". Genome Biology. 14 (10): R115. doi:10.1186/gb-2013-14- ... "Complete mitochondrial genome and evolutionary analysis of Turritopsis dohrnii, the "immortal" jellyfish with a reversible life ...
Consequently, genome stability and regulation of the cell cycle are compromised, contributing to the development of multi-organ ... SON is required for genome stability by ensuring the efficiency of RNA splicing of weak constitutive and alternative splice ... Erroneous SON function causes insufficient production of downstream targets, genome instability and disrupted cell cycle ... Mammalian Genome. 4 (6): 338-342. doi:10.1007/bf00357094. ISSN 0938-8990. PMID 8318737. S2CID 19770065. Livyatan, Ilana; ...
"All Back to Mine: Paul Weller". BBC Genome. 5 February 1998. p. 114. Retrieved 26 March 2019. CS1 maint: discouraged parameter ...
Genome Research. 26 (2): 163-73. doi:10.1101/gr.197517.115. PMC 4728369. PMID 26680994.. ...
The only exception is that the Y chromosome and the mitochondrial genome, both of which are inherited intact from the paternal ... Broman KW (2005). "The genomes of recombinant inbred lines". Genetics. 169 (2): 1133-1146. doi:10.1534/genetics.104.035212. PMC ... Mammalian Genome. 17 (6): 548-564. doi:10.1007/s00335-005-0169-x. PMC 3906707. PMID 16783637. Morahan G, Williams RW (2007). " ... Each strain has a single fixed genome and it is also possible to resample a given genotype multiple times in multiple ...
McHale L, Tan X, Koehl P, Michelmore RW (2006). "Plant NBS-LRR proteins: adaptable guards". Genome Biology. 7 (4): 212. doi: ... Approximately 20 of these proteins have been found in the mammalian genome and include nucleotide-binding oligomerization ... revealed that despite the small number of non-RD kinases in these genomes (9%-29%), 12 of 15 kinases known or predicted to ...
"Draft Genome Sequence of Psychrobacter aquaticus Strain CMS 56T, Isolated from a Cyanobacterial Mat Sample Collected from Water ... Bodies in the McMurdo Dry Valley Region of Antarctica". Genome Announcements. 1 (6): e00918-13. doi:10.1128/genomeA.00918-13. ...
Infection is usually associated either with swimming or with keeping or working with fish (aquarium granuloma). Whole genome ... May 2008). "Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis ... August 2018). "Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing". Scientific ... Genome Announcements. 6 (20). doi:10.1128/genomeA.00397-18. PMC 5958268. PMID 29773624. Das S, Pettersson BM, Behra PR, Mallick ...
Ebert, Dieter (2011-02-04). "A Genome for the Environment". Science. 331 (6017): 539-540. doi:10.1126/science.1202092. ISSN ... Genome Research. 19 (12): 2317-2323. doi:10.1101/gr.096651.109. ISSN 1088-9051. PMC 2792171. PMID 19819907. Bates, Jennifer M ...
For smaller genomes such as Arabidopsis, whole genomes can be examined. Tiling arrays are a useful tool in genome-wide ... Two types of tiling arrays are commonly used for array CGH, whole genome and fine tiled. The whole genome approach would be ... the price makes it impractical to use genome-wide tiling arrays for mammalian and other large genomes. Another issue is the " ... A genome-wide variation of this is known as ChIP-on-chip. Proteins that bind to chromatin are cross-linked in vivo, usually via ...
... at BBC Programmes "LATE-NIGHT SERIAL". BBC Genome. Retrieved 31 January 2019. Book at Bedtime at BBC Programmes ...
Hartley JL, Temple GF, Brasch MA (2001). "DNA Cloning Using In Vitro Site-Specific Recombination". Genome Res. 10 (11): 1788-95 ... Genome Res. 14 (10B): 2136-44. doi:10.1101/gr.2576704. PMC 528930. PMID 15489336. Mehrle A, Rosenfelder H, Schupp I, del Val C ... Genome Res. 11 (3): 422-35. doi:10.1101/gr.GR1547R. PMC 311072. PMID 11230166. Wiemann S, Arlt D, Huber W, Wellenreuther R, ...
What is Genome Editing?. Visit NHGRIs Genome Editing website to learn more about this technology. ... Advances in genome editing technologies made over the past decade allow for precise changes to the DNA code inside of live ... Genome editing technologies present an exciting prospect for treatments and possibly even cures for these diseases. SCGE is ... Genome editing tools need to function specifically on the disease gene to minimize unintended consequences. In addition, the ...
Startup ecosystem development through data. We advise world leaders in policymaking, strategy and actions to drive innovation and economic growth.
As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules are visualized, downloaded, and analyzed by users who range from students to specialized scientists.
Genome definition, a full set of chromosomes; all the inheritable traits of an organism. See more. ... Derived forms of genome. genomic (dʒɪˈnɒmɪk), adjective. Word Origin for genome. C20: from German Genom, from Gen gene + ( ... Words nearby genome. genocopy, genodermatosis, Genoese, genogram, génoise, genome, genomic DNA, genomics, genomic sequencing, ... Other vertebrates have only one copy of a mitochondrial genome.. Lizard-like tuatara carry two distinct mitochondrial genomes, ...
The Human Genome Project. 1460 Words , 6 Pages. Gene Essay Assignment: The Human Genome Project A genome is the complete DNA ... Human Genome Project Essay. 3161 Words , 13 Pages. Human Genome Project Essay The Human Genome Initiative is a worldwide ... Essay On Whole Genome Sequencing. 1226 Words , 5 Pages. *. The Implications Of The Human Genome Project On Human Health. 1853 ... Essay On Whole Genome Sequencing. 1226 Words , 5 Pages. 2.0 Materials and Methods Whole genome sequencing (WGS) is one of the ...
This tool converts genome coordinates and genome annotation files between assemblies. The input data can be pasted into the ... Original Genome: Original Assembly: New Genome: New Assembly: Human. Mouse. A. gambiae. A. mellifera. African clawed frog. ... To lift genome annotations locally on Linux systems, download the liftOver executable and the appropriate chain file. Run ... You must have JavaScript enabled in your web browser to use the Genome Browser ...
Genome Graphs is a tool for displaying genome-wide data sets such as the results of genome-wide SNP association studies, ... browse regions: Takes you to a page with a list of all regions above the significance threshold on the left, and a Genome ... assembly: Specifies which version of the organisms genome sequence to use. *graph ... in ...: Selects which graph(s) to ... For more detailed instructions, see the Genome Graphs Users Guide. *clade: Specifies which clade the organism is in. ...
Genome Graphs is a tool for displaying genome-wide data sets such as the results of genome-wide SNP association studies, ... browse regions: Takes you to a page with a list of all regions above the significance threshold on the left, and a Genome ... assembly: Specifies which version of the organisms genome sequence to use. *graph ... in ...: Selects which graph(s) to ... For more detailed instructions, see the Genome Graphs Users Guide. *clade: Specifies which clade the organism is in. ...
Genome Graphs is a tool for displaying genome-wide data sets such as the results of genome-wide SNP association studies, ... browse regions: Takes you to a page with a list of all regions above the significance threshold on the left, and a Genome ... assembly: Specifies which version of the organisms genome sequence to use. *graph ... in ...: Selects which graph(s) to ... For more detailed instructions, see the Genome Graphs Users Guide. *clade: Specifies which clade the organism is in. ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
Human genomes black holes mapped. 26 March 2018. News. John Sulston obituary: Pioneer genome researcher dies. 9 March 2018. ... Human Genome Project. An international scientific research project with the goal of determining and decoding the total sequence ... Leading Human Genome Project scientist, Sue Povey, dies. 25 February 2019. News. ... Plan to build synthetic human DNA genome gains momentum. 8 May 2017. News. ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
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p,First full sequence of gorilla genome shows 96% share with humans, with close parallels in sensory perception and hearing,/p, ... The genomes of all three species are, in any case, highly similar: humans and chimpanzees share more than 98% of their genes, ... The first full genome analysis has revealed that 15% of gorillas genetic makeup is closer between humans and gorillas than it ... The first full genome analysis has revealed that 15% of gorillas genetic makeup is closer between humans and gorillas than it ...
... however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including ... Most of the enormous genome complexity of pines can be explained by divergence of retrotransposons, ... Evolution of genome size and complexity in Pinus PLoS One. 2009;4(2):e4332. doi: 10.1371/journal.pone.0004332. Epub 2009 Feb 5 ... Genome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes ...
You must have JavaScript enabled in your web browser to use the Genome Browser ... in order to proceed directly to the Genome Browser. For an example page using such links please see the Session Gallery. ... If a saved settings file is available from a web server, you can send email to others with a link such as https://genome.ucsc. ...
You must have JavaScript enabled in your web browser to use the Genome Browser ... in order to proceed directly to the Genome Browser. For an example page using such links please see the Session Gallery. ... If a saved settings file is available from a web server, you can send email to others with a link such as http://genome.ucsc. ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
Life Technologies genome sequencing effort. By BC Staff , May 11, 2000 , 7:00 AM GMT ...
You must have JavaScript enabled in your web browser to use the Genome Browser ...
The Genome Integrity Discussion Group presents meetings featuring talks by graduate students, post-docs, or laboratory heads ... The Genome Integrity Discussion Group meets four to five times each year and provides an opportunity for researchers active in ... Genome Integrity Discussion Group October 2009. Monday, October 5, 2009. The New York Academy of Sciences ...
The Genome Integrity Discussion Group provides a forum for interactions between basic and clinical research groups working on ... The Genome Integrity Discussion Group is proudly supported by. *. *. *. Mission Partner support for the Frontiers of Science ... The Genome Integrity Discussion Group is proudly supported by. *. *. *. Mission Partner support for the Frontiers of Science ... The Genome Integrity meetings are designed to provide a forum for interactions between the many basic science and clinically- ...
UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) Assembly. move <<< title=move 95% to the left>. << title=move 47.5% ... You must have JavaScript enabled in your web browser to use the Genome Browser ...
bROKEN gENOME Page 1 of 1 [15 Posts]. View unread posts. View new posts in the last week. Mark the topic unread :: View ... Posted: Sun Mar 28, 2004 4:31 pm Post subject: bROKEN gENOME. ...
... here has announced a new Environmental Genome Project that will search for human genes that control susceptibility to toxic ... Environmental Genome Project Aims to Find 200 Genes Affected by Toxins. Dec 21, 1998 ... Home » Tools & Technology » Informatics » Environmental Genome Project Aims to Find 200 Genes Affected by Toxins ... Invitae, PCT Therapeutics, Genome Medical Partner to Offer Genetic Testing for Cerebral Palsy. ...
  • A contig is a continu- ous sub-sequence of the genome assembled from sequencing reads. (rutgers.edu)
  • Scaffolding attempts to construct a linear sequence of contigs (with possible gaps in between) using paired reads (two reads whose distance on the genome is approximately known). (rutgers.edu)
  • IMG provides a set of tools for comparative analysis of genes, genomes and functions. (bionity.com)
  • Users can employee a set of powerful tools for comparative analysis and explore the microbial genomes along its 3 main dimensions (genomes, genes and functions), select them and transfer them in the comparative analysis carts. (bionity.com)
  • k-mer counting helps to identify genomic k-mers from sequenced reads which may then inform read correction or genome assembly. (rutgers.edu)
  • The Integrated Microbial Genomes (IMG) is a genome browsing and annotation system developed by the DOE- Joint Genome Institute . (bionity.com)
  • The Integrated Microbial Genomes- Expert Review (IMG/ER) system provides support to individual scientists or group of scientists for functional annotation and curation of their microbial genomes of interest. (bionity.com)
  • Users can submit their annotated genomes (or request the IMG automated annotation pipeline to be applied first) into IMG-ER and proceed with manual curation and comparative analysis in the system, through secure (password protected) access. (bionity.com)
  • We show that current bioinformatic tools are capable of charac- terizing a novel organism by producing a draft genome assembly and gene annotation from single cell data of a MAST-4 stramenopile. (rutgers.edu)
  • Description De novo Genome assembly and k-mer frequency counting are two of the classical prob- lems of Bioinformatics. (rutgers.edu)
  • The Integrated Microbial Genomes with Microbiome Samples (IMG/M) system is an extension of the IMG system providing a comparative analysis context of metagenomic data with the publicly available isolate genomes. (bionity.com)
  • Genome assembly has two major subproblems: contig construction and scaffolding. (rutgers.edu)
  • IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes (including Archaea, Bacteria, Eukarya, Viruses and Plasmids). (bionity.com)
  • It uses material from the Wikipedia article "Integrated_Microbial_Genomes_System" . (bionity.com)
  • Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism. (wikipedia.org)
  • The first genome map of a horse is complete, providing scientists with new tools for investigating equine disease. (uky.edu)
  • But many scientists believe tha genome information will help them find solutions. (uky.edu)
  • In October 1995, 70 scientists from 20 countries met in Lexington, Kentucky to make a plan for mapping the horse genome. (uky.edu)
  • Many scientists have joined forces on the Human Genome Project. (amnh.org)
  • By learning about our genome, scientists will better understand how our bodies work and how diseases develop. (amnh.org)
  • So, to get a complete picture of our species' DNA, you might think that the Human Genome Project scientists have to study the DNA of millions of people -- not even close! (amnh.org)
  • After the entire human genome is sequenced, scientists still won't know which genes control which traits. (amnh.org)
  • Scientists with the Human Genome Project (HGP) study only the human genome. (amnh.org)
  • To understand how our genome works, scientists compare it to the genomes of mice, flies, worms, and even bacteria. (amnh.org)
  • Scientists have released a draft sequence of the orangutan genome, revealing intriguing clues to the evolution of great apes and humans. (bbc.co.uk)
  • A four-year international study of the human genome has prompted scientists to rethink some of their most basic ideas about how DNA functions. (pbs.org)
  • Scientists have assembled the first complete genome of one of humanity's oldest, and least-loved, companions: the bedbug. (amnh.org)
  • Several years ago, U.S. scientists launched a hugely ambitious project called the Cancer Genome Atlas. (ohsu.edu)
  • Scientists have yet to map out the full human genome , so any tests done today are incomplete, as they're missing a fundamental part of indisputable science: a full data set. (healthline.com)
  • Because the process was so slow and required the work of highly skilled technicians, it was clear to most scientists in the mid '80s that it would not be possible to sequence entire genomes by manual methods. (caltech.edu)
  • Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. (redorbit.com)
  • Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism's genome, and might even be responsible for functioning traits. (redorbit.com)
  • The genome has a large number of transposable elements - non-coding parts of the genome that have an important role in gene regulation - that have been moving around in the genome at a relatively rapid pace. (scientificamerican.com)
  • According to Aerts, such knowledge could be extremely useful: "We can now explore if we can use this lock-and-key system to open up or close off other parts of the genome in a controlled way as well. (eurekalert.org)
  • Sequence assembly is especially complicated in plants because some parts of the genome are repeat copies of other parts. (warwick.ac.uk)
  • For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. (wikipedia.org)
  • Depending on the size of the genome or chromosome being built, this may require many rounds of assembly, as the typical starting material for DNA assembly projects is almost always fragments of DNA smaller than 15 kb, with these obtained either from commercial synthesis or from PCR amplification of natural DNA regions. (pnas.org)
  • Bacterial artificial chromosome libraries and BAC-based physical mapping of aquaculture genomes: William S. Davidson. (wiley.com)
  • Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. (wikipedia.org)
  • So while the HGP data may have a gene and a sequence, but not a structure, [email protected] might have a protein and a structure, and if their structures match, then it's very likely that the relationship between genome and protein has been found. (wired.com)
  • For example, if an unclassified genome has the same sequence as a protein used in digestion, then it's possible that the gene is also used in digestion. (wired.com)
  • It is important to consider how the genome is similar to other genomes that are already known, as this can help when establishing the role of the gene. (news-medical.net)
  • The efficiency, versatility and multiplexing capacity of RNA-guided genome engineering using the CRISPR/Cas9 technology enables a variety of applications in plants, ranging from gene editing to the constructi. (biomedcentral.com)
  • Physical and gene map of the green alga Nephroselmis chloroplast genome, showing the typical structural arrangement found in land plants. (tolweb.org)
  • This greatly simplifies the process of gene editing by allowing for rapid, efficient and precise engineering, even with complex genomes. (prweb.com)
  • This Hub is maintained as a result of the gene editing project of the OECD Working Party on Biotechnology, Nanotechnology and Converging Technologies (BNCT ) which is a partner in the genome editing conference. (oecd.org)
  • Given the massive amount of population-based data that will be generated over the next decades, we believe a coordinated global effort is needed to disseminate human genome epidemiologic information in order to keep up with the progress of the Human Genome Project and its accompanying gene discoveries. (cdc.gov)
  • Now that we can systematically profile genomes, epigenomes and transcriptomes, the challenge is to discover the rules that link DNA sequence with chromatin state and gene expression. (eurekalert.org)
  • They shared a vision of the future in which knowledge of every gene that composes the human genome would be available to any scientist in the world at the click of a computer key. (caltech.edu)
  • We will look at the basic molecular and cellular processes underlying gene expression, genome structure and evolution as well as the techniques used to study them. (le.ac.uk)
  • Once considered a speciation process common only in plants, polyploidy is now recognized to have played a major role in the structure, gene content, and evolution of most eukaryotic genomes. (springer.com)
  • El-Mabrouk, N.: Genome rearrangements with gene families. (springer.com)
  • The work is published in Genome Biology . (epfl.ch)
  • Genome Biology 18:149, 7 August 2017. (epfl.ch)
  • The human genome project changed biology forever. (uky.edu)
  • The journal Genome Biology is published by BioMedCentral, and offers free access to primary research articles and a preprint depository to which authors may submit work for free distribution over the web. (scidev.net)
  • Genome-scale plant research to address fundamental questions in biology, including processes of economic and/or societal importance. (nsf.gov)
  • The Ohio State report was published today on the website of the journal Genome Biology. (eurekalert.org)
  • A second key invention for the genome project was developed at Caltech by Professor Melvin Simon, chair of Caltech's biology division, and his coworker Hiroaki Shizuya. (caltech.edu)
  • Genome rearrangement problems have proved so interesting from a combinatorial point of view that the field now belongs as much to mathematics as to biology. (mit.edu)
  • Genome: The Autobiography of a Species in 23 Chapters is a 1999 popular science book by the science writer Matt Ridley , published by Fourth Estate. (wikipedia.org)
  • It would be very valuable to sequence more primate genomes to enable more comparative analysis of this kind and thus help us understand the evolution of primates and our own species. (bbc.co.uk)
  • A "first draft" of the Neanderthal genome announced today adds to evidence that the extinct human species was lactose intolerant and could have shared some basic language capabilities with modern humans. (nationalgeographic.com)
  • By contrast, a genome is the full set of genes that gives rise to a particular species. (nationalgeographic.com)
  • And now, we've found at least one species where the parasite's entire or nearly entire genome has been absorbed and integrated into the host's. (redorbit.com)
  • Published today in the open-access journal GigaScience , is an article that presents the genome sequence of Ginkgo biloba , the oldest extant tree species. (eurekalert.org)
  • Given its longevity as a species and unique position in the evolutionary tree of life, the ginkgo genome will provide an extensive resource for studies concerning plant defenses against insects and pathogens, and research investigating early events in tree evolution and in evolution overall. (eurekalert.org)
  • The tree's genome is also larger than other plant species known for extremely big genomes, such as maize or orchids. (eurekalert.org)
  • Combinatorial methods are used to reconstruct putative rearrangement scenarios in order to explain the evolutionary history of a set of species, often formalizing the evolutionary events that can explain the multiple combinations of observed genomes as combinatorial optimization problems. (mit.edu)
  • The traditional method of curation method uses the Basic Local Alignment Search Tool (BLAST) algorithm to find similarities to annotate the genome. (news-medical.net)
  • There is a general conception that we can only find meaningful differences by surveying the entire genome," said Bejerano. (stanford.edu)
  • When Bob Waterston became chair of the Department of Genome Sciences in 2002, it was a major coup for UW Medicine. (washington.edu)
  • Confusion was enhanced when the human genome was compared to a yeast cell with 6,000 genes, a fly with 13,000 genes, a worm with 26,000 genes, and a rice cell with 50,000 genes. (encyclopedia.com)
  • The project to sequence the yeast genome got underway in 1989 and the entire code of strain S288c was spelled out in 1996. (brighthub.com)
  • It was extracted from its yeast host and used to transform Mycoplasma cells, resulting in a bacteria growing and dividing with the accepted synthetic genome. (pnas.org)
  • These repeats can be thousands of nucleotides long, and some occur in thousands of different locations, especially in the large genomes of plants and animals. (wikipedia.org)
  • However, by stepping down a scale from bacteria to viruses, opportunities quickly arise, even for those viruses with comparatively large genomes, like the double-stranded DNA herpes simplex virus (HSV) type 1 genome, over 150 kb in length. (pnas.org)
  • In a recent interview, Dr. Waterston talked about his career and genome sciences. (washington.edu)
  • Dr. Kelley Harris joined Genome Sciences in 2018. (washington.edu)
  • Genome Sciences is pleased to welcome Dr. Brian Beliveau to the department in September 2018 as our newest faculty member. (washington.edu)
  • Retrieved on December 14, 2019 from https://www.news-medical.net/life-sciences/Genome-Analysis.aspx. (news-medical.net)
  • Retrieved on August 17, 2019 from https://www.news-medical.net/life-sciences/Lentivirus-Genome.aspx. (news-medical.net)
  • Genome mapping in animals is now one of the leading disciplines in animal sciences. (springer.com)
  • Say Hello to Chip Skowron III, the Latest Hedge-Funder Charged With Insider Trading [Updated] Over a tip about Human Genome Sciences. (nymag.com)
  • In Caltech's Division of the Humanities and Social Sciences, Professor Daniel Kevles has examined these ethical issues in his book The Code of Codes: Scientific and Social Issues in the Human Genome Project, which he coedited in 1992 with Leroy Hood. (caltech.edu)
  • and FST values were significantly higher for SNPs within the Batwa pygmy phenotype-associated regions than the remainder of the genome, a signature of polygenic adaptation. (ebi.ac.uk)
  • 65 participants at the 2016 NIST Genome Editing Standards Workshop identified pre-competitive standards and measurements needed to establish greater confidence in characterization of genome editing outputs. (nist.gov)
  • In 2016, the same strategy allowed the Venter Institute team to construct a working, rationally reduced Mycoplasma genome with large-scale changes from the natural sequence, including removal of hundreds of genes ( 12 ). (pnas.org)
  • Groundbreaking Journal, Gender and the Genome, To Launch in Summer 2016. (liebertpub.com)
  • DNA sequence assembly involves the alignment and merging of DNA fragments to reconstruct the DNA so that smaller sections of the genome can be analyzed. (news-medical.net)
  • The book also discusses an important generalization of the basic problem known as the median problem, surveys attempts to reconstruct the relationships between genomes with phylogenetic trees, and offers a collection of summaries and appendixes with useful additional information. (mit.edu)
  • Getting an effectively complete genome sequence of a bacterium that lived nearly 700 years ago is incredibly exciting,' said Julian Parkhill, a disease genome expert at the Wellcome Trust Sanger Institute in Britain. (cbc.ca)
  • This book will be a defining book for the field of genome rearrangement and is destined to become a classic as soon as it hits the bookshelves. (mit.edu)
  • It presents a series of models, beginning with the simplest (which is progressively extended by dropping restrictions), each constructing a genome rearrangement problem. (mit.edu)
  • The NIST-led Genome Editing Consortium has been established to address these needs. (nist.gov)
  • As of December 2017, Mary Ann Liebert, Inc. is no longer the publisher of Gender and the Genome , The Official Journal of the Foundation for Gender-Specific Medicine. (liebertpub.com)
  • This genome-wide, high-resolution analysis of the partitioning of chloroplast ribosomes between membrane and soluble fractions revealed that approximately half of the chloroplast-encoded thylakoid proteins integrate cotranslationally and half integrate posttranslationally. (pnas.org)
  • An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. (wikipedia.org)
  • Pre-processing refers to generating analysis-ready mapped reads from raw reads using tools like BWA*, Picard* tools, and the Genome Analysis Tool Kit. (intel.com)
  • The analysis of DNA phase is the final step in genome analysis. (news-medical.net)
  • The team's analysis reveals that the orangutan genome has experienced a slower rate of evolution than those of other great apes, with fewer rearrangements, duplications and repeats in the sequence. (bbc.co.uk)
  • Ending one long-standing argument, analysis of the coelacanth genome clearly shows that it is not the closest living fishy relative to tetrapods, Amemiya says: that honor belongs to the lungfish. (scientificamerican.com)
  • The analysis showed that not all parts of the coelacanth genome are slow to evolve. (scientificamerican.com)
  • Surprisingly, there is a lack of genome analysis data in literature against CNS particularly of human origin. (omicsonline.org)
  • It is employed for all facets in genome analysis in animals and their improvement for benefit of human beings. (springer.com)
  • The Social Genome Project , a model of social mobility over the life cycle, will produce a unique new data set and tool for policy analysis. (brookings.edu)
  • Here we describe a protocol for large-scale genome-wide analysis that facilitates quality control and population stratification correction in 9K, 13K, and 23K individuals while maintaining the confidentiality of underlying genotypes and phenotypes. (virginia.edu)
  • Isaacs and Church also showed that eliminating the UAG codon frees up a protein coding space in an organism's genome, allowing for a more efficient incorporation of non-standard amino acids - amino acids that are not traditionally coded for. (yaledailynews.com)
  • Meanwhile, Bailey wants to sequence the genome of a patient's cancer? (go.com)
  • I understood that they a) made a map, and b) intend to sequence the genome over the next year. (scienceblogs.com)
  • According to the article at www.sciencedaily.com they didn't sequence the genome yet. (scienceblogs.com)
  • The Cancer Genome Atlas is the outgrowth of a year and a half of planning by NIH advisory groups. (washingtonpost.com)
  • The size of the bovine genome is 3 Gb (3 billion base pairs ). (wikipedia.org)
  • Jinni's Movie Genome has a taxonomy created by film professionals, while titles are automatically indexed using a mixture of metadata and reviews and a proprietary Natural Language Processing solution to assign semantic tags to content and users. (wikipedia.org)
  • The data about each title in a Movie Genome can also support an item-based recommendation engine that recommends based on similarities between content items and users' preferred "genes. (wikipedia.org)
  • If we pick a disease to treat using genome editing, we should start with something relatively simple," he says. (technologyreview.com)
  • Targeted genome editing, a method used to alter the DNA of living cells at desired locations, is poised to revolutionize science and medicine. (nist.gov)
  • NIST has brought together experts across the genome editing field including stakeholders in industry, academia and government to assess their measurement needs. (nist.gov)
  • These discussions have identified common pre-competitive measurements and standards needed to establish greater confidence in the characterization of genome editing outputs. (nist.gov)
  • Design and conduct controlled evaluations of existing assays for quantifying on- and off-target genome editing, with a robust and optimal experimental design aimed at assessing the sources of variability, repeatability, and reproducibility within an assay. (nist.gov)
  • Determine the type of metadata that would be needed to be shared, housed, and interrogated from genome editing experiments. (nist.gov)
  • Identify terms and related definitions to form a common genome editing community lexicon. (nist.gov)
  • The efficiency of multiplex editing in plants by the RNA-guided Cas9 system is limited by efficient introduction of its components into the genome and by their activity. (biomedcentral.com)
  • By co-expressing two guide RNAs using dual RNA polymerase promoters, the patent-pending NickaseNinja removes the need for co-transfection of multiple vectors, improving genome editing efficiency and consistency compared with the conventional two vector systems currently available. (prweb.com)
  • The OECD Conference on Genome Editing: Applications in Agriculture - Implications for Health, Environment and Regulation explored the safety and regulatory considerations raised by genome edited products, with the aim to favour a coherent policy approach to facilitate innovation involving genome editing and will bring together policy makers, academia, innovators and other stakeholders involved in the topic. (oecd.org)
  • Genome editing - set of techniques in which specialised enzymes have been modified - can insert, replace or remove DNA from a genome with a high degree of specificity. (oecd.org)
  • The rapidly growing use of genome editing has policy implications and human health and environmental safety considerations. (oecd.org)
  • The meeting report of the OECD conference on ''Genome Editing: Applications in Agriculture-Implications for Health, Environment and Regulation'' includes in-depth summaries of the presentations of each invited speaker given at the Conference. (oecd.org)
  • The Policy Considerations Regarding Genome Editing describes the applications of genome editing, its risk and safety considerations and regulatory aspects. (oecd.org)
  • This session presented background information on genome editing techniques in the broader context. (oecd.org)
  • Science and Legal Experts Debate Future Uses and Impact of Human Genome Editing in Gender and the Genome. (liebertpub.com)
  • Human Genome Variation is delighted to present its first Collection for the March 2019 issue. (nature.com)
  • Everyone on the planet -- except identical twins -- has a unique genome. (amnh.org)
  • Through this route in 2010, the J. Craig Venter Institute constructed the first completely synthetic bacterial genome ( 2 ). (pnas.org)
  • The 8th Dorothy Russell Havemeyer Foundation International Equine Genome Mapping Workshop took place near Newmarket, UK from July 22 to 25, 2009. (uky.edu)
  • The series Genome Mapping in Animals will fill this gap. (springer.com)
  • Proteins in the chloroplast thylakoid membrane system are derived from both the nuclear and plastid genomes. (pnas.org)
  • Chloroplast genomes encode ∼37 proteins that integrate into the thylakoid membrane. (pnas.org)
  • Whereas [email protected] is designed to learn how genomes fold into proteins, [email protected] was launched this week to try and reverse engineer known proteins by guessing the genome sequence of their structures. (wired.com)
  • This effort is very much a discovery for the participants, as learning how genomes become proteins is something that's still largely unknown. (wired.com)
  • The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). (wikipedia.org)
  • David Reich/Nature The entire genome of the Denisovans was extracted from a tooth and finger bone. (scienceblogs.com)
  • A plan was made to sequence the entire human genome in the late 1980s. (uky.edu)
  • and the University of Tubingen in Germany describe its entire genome. (cbc.ca)
  • But integrating an entire genome was definitely an unexpected find. (redorbit.com)
  • Insights into the architecture of ancestral chloroplast genomes. (tolweb.org)
  • We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. (ebi.ac.uk)
  • When the human genome was fully sequenced in 2001, it was hailed as a remarkable achievement. (stanford.edu)

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