Expressed Sequence Tags: Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Sequence Tagged Sites: Short tracts of DNA sequence that are used as landmarks in GENOME mapping. In most instances, 200 to 500 base pairs of sequence define a Sequence Tagged Site (STS) that is operationally unique in the human genome (i.e., can be specifically detected by the polymerase chain reaction in the presence of all other genomic sequences). The overwhelming advantage of STSs over mapping landmarks defined in other ways is that the means of testing for the presence of a particular STS can be completely described as information in a database.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Gene Expression Profiling: The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.Databases, Genetic: Databases devoted to knowledge about specific genes and gene products.Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Genes, Plant: The functional hereditary units of PLANTS.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Databases, Nucleic Acid: Databases containing information about NUCLEIC ACIDS such as BASE SEQUENCE; SNPS; NUCLEIC ACID CONFORMATION; and other properties. Information about the DNA fragments kept in a GENE LIBRARY or GENOMIC LIBRARY is often maintained in DNA databases.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Oligonucleotide Array Sequence Analysis: 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.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Genomics: The systematic study of the complete DNA sequences (GENOME) of organisms.Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)RNA, Messenger: 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.Genetic Markers: A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.RNA, Plant: Ribonucleic acid in plants having regulatory and catalytic roles as well as involvement in protein synthesis.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Databases, Factual: Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.Molecular Sequence Annotation: The addition of descriptive information about the function or structure of a molecular sequence to its MOLECULAR SEQUENCE DATA record.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Oryza sativa: 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.Arabidopsis: 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.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Internet: A loose confederation of computer communication networks around the world. The networks that make up the Internet are connected through several backbone networks. The Internet grew out of the US Government ARPAnet project and was designed to facilitate information exchange.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.Plant Structures: The parts of plants, including SEEDS.Triticum: A plant genus of the family POACEAE that is the source of EDIBLE GRAIN. A hybrid with rye (SECALE CEREALE) is called TRITICALE. The seed is ground into FLOUR and used to make BREAD, and is the source of WHEAT GERM AGGLUTININS.Blotting, Northern: Detection of RNA 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.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Transcriptome: The pattern of GENE EXPRESSION at the level of genetic transcription in a specific organism or under specific circumstances in specific cells.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Radiation Hybrid Mapping: A method for ordering genetic loci along CHROMOSOMES. The method involves fusing irradiated donor cells with host cells from another species. Following cell fusion, fragments of DNA from the irradiated cells become integrated into the chromosomes of the host cells. Molecular probing of DNA obtained from the fused cells is used to determine if two or more genetic loci are located within the same fragment of donor cell DNA.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.User-Computer Interface: The portion of an interactive computer program that issues messages to and receives commands from a user.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Plant Diseases: Diseases of plants.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.Polymorphism, Single Nucleotide: A single nucleotide variation in a genetic sequence that occurs at appreciable frequency in the population.Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Untranslated Regions: The parts of the messenger RNA sequence that do not code for product, i.e. the 5' UNTRANSLATED REGIONS and 3' UNTRANSLATED REGIONS.Plant Roots: The usually underground portions of a plant that serve as support, store food, and through which water and mineral nutrients enter the plant. (From American Heritage Dictionary, 1982; Concise Dictionary of Biology, 1990)Ophthalmology: A surgical specialty concerned with the structure and function of the eye and the medical and surgical treatment of its defects and diseases.Zea mays: A plant species of the family POACEAE. It is a tall grass grown for its EDIBLE GRAIN, corn, used as food and animal FODDER.Lens Plant: A plant genus of the FABACEAE family known for the seeds used as food.Lotus: A plant genus of the family FABACEAE. This genus was formerly known as Tetragonolobus. The common name of lotus is also used for NYMPHAEA and NELUMBO.Helminth Proteins: Proteins found in any species of helminth.Algorithms: A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.Coffea: A plant genus of the family RUBIACEAE. It is best known for the COFFEE beverage prepared from the beans (SEEDS).Sorghum: 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.DNA, Helminth: Deoxyribonucleic acid that makes up the genetic material of helminths.Gene Expression Regulation: 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.Algal Proteins: Proteins found in any species of algae.Exons: 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.Solanaceae: A plant family of the order Solanales, subclass Asteridae. Among the most important are POTATOES; TOMATOES; CAPSICUM (green and red peppers); TOBACCO; and BELLADONNA.Genes, Insect: The functional hereditary units of INSECTS.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Saccharum: A plant genus of the family POACEAE widely cultivated in the tropics for the sweet cane that is processed into sugar.Introns: 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.Insect Proteins: Proteins found in any species of insect.Genome, Helminth: The genetic complement of a helminth (HELMINTHS) as represented in its DNA.Fragaria: A plant genus of the family ROSACEAE known for the edible fruit.Synteny: 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.Organ Specificity: Characteristic restricted to a particular organ of the body, such as a cell type, metabolic response or expression of a particular protein or antigen.Nematoda: A class of unsegmented helminths with fundamental bilateral symmetry and secondary triradiate symmetry of the oral and esophageal structures. Many species are parasites.High-Throughput Nucleotide Sequencing: Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.Mycelium: The body of a fungus which is made up of HYPHAE.Rhodophyta: Plants of the division Rhodophyta, commonly known as red algae, in which the red pigment (PHYCOERYTHRIN) predominates. However, if this pigment is destroyed, the algae can appear purple, brown, green, or yellow. Two important substances found in the cell walls of red algae are AGAR and CARRAGEENAN. Some rhodophyta are notable SEAWEED (macroalgae).Genome, Fungal: The complete gene complement contained in a set of chromosomes in a fungus.Plant Leaves: Expanded structures, usually green, of vascular plants, characteristically consisting of a bladelike expansion attached to a stem, and functioning as the principal organ of photosynthesis and transpiration. (American Heritage Dictionary, 2d ed)Cicer: A plant genus of the family FABACEAE known for the edible beans.Rosaceae: The rose plant family in the order ROSALES and class Magnoliopsida. They are generally woody plants. A number of the species of this family contain cyanogenic compounds.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Seeds: The encapsulated embryos of flowering plants. They are used as is or for animal feed because of the high content of concentrated nutrients like starches, proteins, and fats. Rapeseed, cottonseed, and sunflower seed are also produced for the oils (fats) they yield.Chromosomes, Artificial, Yeast: Chromosomes in which fragments of exogenous DNA ranging in length up to several hundred kilobase pairs have been cloned into yeast through ligation to vector sequences. These artificial chromosomes are used extensively in molecular biology for the construction of comprehensive genomic libraries of higher organisms.Flowers: The reproductive organs of plants.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Gene Expression Regulation, Developmental: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action during the developmental stages of an organism.

*  Oliz, a suite of Perl scripts that assist in the design of microarrays using 50mer oligonucleotides from the 3' untranslated...

... and the availability of sequence information (in the form of Expressed Sequence Tags, ESTs). ... Blastn lists genes with significant sequence similarity to the query sequence. However, only the portion of the sequence that ... Due to the high error rate in both the sequence and annotation of ESTs, clusters contains only one EST sequence are excluded ... the complete sequence for each match was retrieved and then truncated to a 50mer corresponding to the query sequence. Those ...
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-3-27

*  Isolation of Differentially Expressed Sequence Tags from Human Breast Cancer | Cancer Research

Isolation of Differentially Expressed Sequence Tags from Human Breast Cancer. Mark A. Watson and Timothy P. Fleming ... Isolation of Differentially Expressed Sequence Tags from Human Breast Cancer Message Subject (Your Name) has forwarded a page ... we describe the isolation of differentially expressed sequence tags, short complementary DNA fragments corresponding to mRNAs ... Direct sequencing and expression analysis of two sequence tags demonstrate that they represent sequences which are ...
cancerres.aacrjournals.org/content/54/17/4598

*  Sequencing, Analysis, and Annotation of Expressed Sequence Tags for Camelus dromedarius

... Abdulaziz M. Al-Swailem,1 Maher M. ... Parkinson J, Blaxter M. Expressed sequence tags: an overview. Methods Mol Biol. 2009;533:1-12. [PubMed] ... When such a sequence is found, we calculated the lengths of the subsequences after the chimeric sequence is divided into two or ... If the remaining sequence after the clean-up procedure was less than 100 base pairs (bp), we eliminated the sequence from ...
pubmedcentralcanada.ca/pmcc/articles/PMC2873428/

*  Sabinet | Algorithms for clustering expressed sequence tags : the wcd tool : reviewed article

Expressed Sequence Tags (ESTs) are a technology used to explore the transcriptome (a record of this gene activity). ESTs are ... Expressed Sequence Tags (ESTs) are a technology used to explore the transcriptome (a record of this gene activity). ESTs are ... n South African Computer Journal - Algorithms for clustering expressed sequence tags : the wcd tool : reviewed article * ... Keyword(s) : Clustering, D2, Expressed sequence tags, Heuristics, Strings and Suffix arrays ...
journals.co.za/content/comp/2008/40/EJC28046

*  Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially...

Expressed sequence tags from larval gut of the European corn borer (Ostrinia nubilalis): Exploring candidate genes potentially ... Only a few studies have focused on developing expressed sequence tag (EST) libraries from the guts of lepidopteran larvae. ... Knowledge of the genes that are expressed in the insect gut are crucial for understanding basic physiology of food digestion, ... Among the unique sequences, 62.7% encoded putative proteins that shared significant sequence similarities (E-value ≤ 10-3)with ...
pubmedcentralcanada.ca/pmcc/articles/PMC2717985/?report=abstract

*  Dna(branchiostoma floridae clone mpmgp498n0544 est(expressed sequence tag))(9ci) - Alfa Chemistry

... expressed sequence tag)) (9CI)),please inquire us for 523341-81-3(DNA(Branchiostoma floridae clone MPMGp498N0544 EST (expressed ... Home > Product > Heterocyclic Organic Compounds > Dna(branchiostoma floridae clone mpmgp498n0544 est(expressed sequence tag))( ... Dna(branchiostoma floridae clone mpmgp498n0544 est(expressed sequence tag))(9ci) , CAS Number: 523341-81-3. ...
alfa-chemistry.com/cas_523341-81-3.htm

*  Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: The first transcriptome analysis of an Anguinid...

Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: The first transcriptome analysis of an Anguinid ... Expressed sequence tags of the peanut pod nematode Ditylenchus africanus: The first transcriptome analysis of an Anguinid ... In this study, 4847 expressed sequenced tags (ESTs) from mixed stages of the migratory plant-parasitic nematode Ditylenchus ... Other tags showed homology to genes previously described as being involved in parasitism (expansin, SEC-2, calreticulin, 14-3- ...
eprints.ugd.edu.mk/2611/

*  The Plant Genome - Original Research Parallel Sequencing of Expressed Sequence Tags from Two Complementary DNA Libraries for...

Distribution of expressed sequence tag Blastx hits in terms of E-value for the expressed sequence tags (ESTs) from the ... Expressed sequence tags make up a grand proportion of the GenBank nucleotide sequence collection (Benson et al., 2008). ... Expressed sequence tags differentially expressed in the DOR364 libraries would be expected to represent early responses to P ... The number of gene ontologies for each expressed sequence tag (EST) sequences found during the EST sequence annotation ...
https://dl.sciencesocieties.org/publications/tpg/articles/4/3/204

*  Opium poppy and Madagascar periwinkle: model non-model systems to investigate alkaloid biosynthesis in plants - Facchini - 2008...

Murata, J., Bienzle, D., Brandle, J.E., Sensen, C.W. and De Luca, V. (2006) Expressed sequence tags from Madagascar periwinkle ... Expressed sequence tags. Compared with model plants such as Arabidopsis, rice and tomato, the number of ESTs for alkaloid- ... Nevertheless, application of high-throughput technologies such as genome sequencing, expressed sequence tag (EST) and DNA ... McKnight, T.D., Roessner, C.A., Devagupta, R., Scott, A.I. and Nessler, C.L. (1990) Nucleotide sequence of a cDNA encoding the ...
onlinelibrary.wiley.com/doi/10.1111/j.1365-313X.2008.03438.x/full

*  Author Page for Matthew Rimmer :: SSRN

The New Conquistadors: Patent Law and Expressed Sequence Tags Journal of Law, Information, and Science, Vol. 16, p. 10-50, 2007 ...
https://papers.ssrn.com/sol3/cf_dev/AbsByAuth.cfm?per_id=358042

*  Download Free easiEST, easiEST 0.3 Download

BSEditor: A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. It contains functionalities of ESTs for ... Tags. 5.2.7.2 anydvd , gt legends support , htc hd7 g1 , convert img to , google ipod converter , easiest backup , htc radar 4g ...
brothersoft.com/easiest-297411.html

*  Food and Agriculture

Kiwi Fruit's Expressed Sequence Tags Published. New Zealand-based fruit science company HortResearch and Genesis Research and ... Azotobacter vinelandii Genome Sequence. Researchers have successfully sequence the genome of Azotobacter vinelandii, a nitrogen ...
biotech-weblog.com/category/food-and-agriculture/

*  Global Rejection of Genetically Engineered Wheat - BioTech Weblog

Kiwi Fruit's Expressed Sequence Tags Published. Leave A Reply Cancel Reply. Notify me of follow-up comments by email. ...
biotech-weblog.com/global-rejection-of-genetically-engineered-wheat/

*  Lunar Greenhouse: Growing Food Fit For The Moon - BioTech Weblog

Kiwi Fruit's Expressed Sequence Tags Published. Leave A Reply Cancel Reply. Notify me of follow-up comments by email. ...
biotech-weblog.com/lunar-greenhouse-growing-food-fit-for-the-moon/

*  Fish and chips: functional genomics of social plasticity in an African cichlid fish | Journal of Experimental Biology

expressed sequence tags. FDR. false discovery rate. GABA. gamma-aminobutyric acid. GH. growth hormone. GHRH. growth hormone- ... Annotation of expressed sequence tags for the East African cichlid fish species Astatotilapia burtoni and evolutionary analyses ... resulting in 4258 expressed sequence tags (ESTs), 3670 of which were deemed to be of high quality and have been submitted to ... among the three GnRH neuropeptide genes that are expressed in the brain of fish, only GnRH1, the form expressed in the POA ( ...
jeb.biologists.org/content/211/18/3041

*  Difference between revisions of "User:Jarle Pahr/Bioinformatics" - OpenWetWare

Expressed Sequence Tags (EST): Serial Analysis of Gene Expression (SAGE): Expression quantitive trait loci (eQTLs) ... Sequence databases: NCBI Sequence Read Archive (SRA): http://www.ncbi.nlm.nih.gov/sra Stores raw sequencing data from high- ... Structure predictions are made by "threading" (aligning) each amino acid in the target sequence to one of several templates and ... The unit PAM (Point Accepted Mutations) measures the number of retained mutations in a sequence. ...
https://openwetware.org/wiki/?title=User:Jarle_Pahr/Bioinformatics&curid=131931&diff=706506&oldid=706122

*  Genome-Wide Survey for Biologically Functional Pseudogenes

Expressed sequence tags Is the Subject Area "Expressed sequence tags" applicable to this article? Yes. No. ... Sequence alignment Is the Subject Area "Sequence alignment" applicable to this article? Yes. No. ... Sequence databases Is the Subject Area "Sequence databases" applicable to this article? Yes. No. ...
journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020046

*  zn18a12.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA - EST - NCBI

You are here: NCBI , DNA & RNA , Database of Expressed Sequence Tags (dbEST) ... zn18a12.s1 Stratagene neuroepithelium NT2RAMI 937234 Homo sapiens cDNA clone IMAGE:547774 3-, mRNA sequence. GenBank: ... Find regions of similarity between this sequence and other sequences using BLAST. ...
https://ncbi.nlm.nih.gov/nucest/AA084615?report=genbank

*  DKFZp470E1711 r1 470 (synonym: pliv1) Pongo abelii cDNA clone DKFZp470 - EST - NCBI

You are here: NCBI , DNA & RNA , Database of Expressed Sequence Tags (dbEST) ... DKFZp470E1711_r1 470 (synonym: pliv1) Pongo abelii cDNA clone DKFZp470E1711 5-, mRNA sequence. GenBank: CR524568.1 ... Find regions of similarity between this sequence and other sequences using BLAST. ...
https://ncbi.nlm.nih.gov/nucest/49682791

*  Plus it

the two most popular ways of cataloging human genes are sequencing expressed sequence tags (ESTs) and utilization of ... Rougeon F, Kourilsky P, and Mach B. Insertion of a rabbit beta-globin gene sequence into an E. coli plasmid. Nucleic Acids Res ... Liu X and Mertz JE. HnRNP L binds a cis-acting RNA sequence element that enables intron-dependent gene expression. Genes Dev 9 ... In many cases, one can predict in silico the largest ORF of an mRNA from cDNA sequence, based on the presence of an AUG codon ...
physiolgenomics.physiology.org/content/6/2/57

*  Plus it

... expressed sequence tag; polyoma mT, polyoma middle T antigen; FCS, fetal calf serum; nt, nucleotide; D000, 3-(2-chlorophenyl)-2 ... These cells express all of the class IA p110 isoforms (Fig. 2B) ⇓ and display positive chemotaxis toward EGF. When incubated ... In addition to p110α and p110β, these cells express p110δ at levels similar to those seen in WBCs (Fig. 2B) ⇓ . MDA-MB-231 ... Previous studies indicated that p110α and p110β mRNAs are broadly but not uniformly expressed (36 , 46 , 47) , whereas p110δ ...
cancerres.aacrjournals.org/content/63/7/1667

*  Chemoattractant Receptor-Homologous Molecule Expressed on Th2 Cells Activation in Vivo Increases Blood Leukocyte Counts and Its...

... expressed sequence tag; PCR, polymerase chain reaction; PBS, phosphate-buffered saline; RT-PCR, reverse transcription-PCR; ... Rat CRTH2 cDNA gene sequence. Full cDNA sequence of the rat CRTH2 gene. The sequence is available under GenBank accession ... Rat CRTH2 cDNA amino acid sequence alignment. Amino acid sequence alignment of human, mouse, and rat CRTH2. Identical residues ... and the full cDNA sequence is shown in Fig. 1. The sequence of the rat CRTH2 protein bears 89% identity with mouse CRTH2 and 75 ...
jpet.aspetjournals.org/content/307/2/518

*  Publication : USDA ARS

Title: EXPRESSED SEQUENCE TAGS FROM DEVELOPMENTAL STAGES OF GIBBERELLA ZEAE Author Trail, Frances ...
https://ars.usda.gov/research/publications/publication/?seqNo115=128236

Sequence clustering: In bioinformatics, sequence clustering algorithms attempt to group biological sequences that are somehow related. The sequences can be either of genomic, "transcriptomic" (ESTs) or protein origin.Library (biology): In molecular biology, a library is a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. There are different types of DNA libraries, including cDNA libraries (formed from reverse-transcribed RNA), genomic libraries (formed from genomic DNA) and randomized mutant libraries (formed by de novo gene synthesis where alternative nucleotides or codons are incorporated).Coles PhillipsDNA sequencer: A DNA sequencer is a scientific instrument used to automate the DNA sequencing process. Given a sample of DNA, a DNA sequencer is used to determine the order of the four bases: G (guanine), C (cytosine), A (adenine) and T (thymine).Gene signature: A gene signature is a group of genes in a cell whose combined expression patternItadani H, Mizuarai S, Kotani H. Can systems biology understand pathway activation?Extracellular: In cell biology, molecular biology and related fields, the word extracellular (or sometimes extracellular space) means "outside the cell". This space is usually taken to be outside the plasma membranes, and occupied by fluid.Protein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Symmetry element: A symmetry element is a point of reference about which symmetry operations can take place. In particular, symmetry elements can be centers of inversion, axes of rotation and mirror planes.Chromosome regionsCS-BLASTLigation-independent cloning: Ligation-independent cloning (LIC) is a form of molecular cloning that is able to be performed without the use of restriction endonucleases or DNA ligase. This allows genes that have restriction sites to be cloned without worry of chopping up the insert.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.Branching order of bacterial phyla (Gupta, 2001): There are several models of the Branching order of bacterial phyla, one of these was proposed in 2001 by Gupta based on conserved indels or protein, termed "protein signatures", an alternative approach to molecular phylogeny. Some problematic exceptions and conflicts are present to these conserved indels, however, they are in agreement with several groupings of classes and phyla.Cellular microarray: A cellular microarray is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as antibodies, proteins, or lipids, which can interact with the cells, leading to their capture on specific spots.Squamosa promoter binding protein: The SQUAMOSA promoter binding protein-like (SBP or SPL) family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene.Ontario Genomics Institute: The Ontario Genomics Institute (OGI) is a not-for-profit organization that manages cutting-edge genomics research projects and platforms.The Ontario Genomics Institute OGI also helps scientists find paths to the marketplace for their discoveries and the products to which they lead, and it works through diverse outreach and educational activities to raise awareness and facilitate informed public dialogue about genomics and its social impacts.ParaHox: The ParaHox gene cluster is an array of homeobox genes (involved in morphogenesis, the regulation of patterns of anatomical development) from the Gsx, Xlox (Pdx) and Cdx gene families.Mature messenger RNA: Mature messenger RNA, often abbreviated as mature mRNA is a eukaryotic RNA transcript that has been spliced and processed and is ready for translation in the course of protein synthesis. Unlike the eukaryotic RNA immediately after transcription known as precursor messenger RNA, it consists exclusively of exons, with all introns removed.Microsatellite: A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 2–5 base pairs) are repeated, typically 5-50 times. Microsatellites occur at thousands of locations in the human genome and they are notable for their high mutation rate and high diversity in the population.Mac OS X Server 1.0List of sequenced eukaryotic genomesOpen reading frame: In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).Weedy rice: Weedy rice, also known as red rice, is a variety of rice (Oryza) that produces far fewer grains per plant than cultivated rice and is therefore considered a pest. The name "weedy rice" is used for all types and variations of rice which show some characteristic features of cultivated rice and grow as weeds in commercial rice fields.GAI (Arabidopsis thaliana gene)Molecular evolution: Molecular evolution is a change in the sequence composition of cellular molecules such as DNA, RNA, and proteins across generations. The field of molecular evolution uses principles of evolutionary biology and population genetics to explain patterns in these changes.Internet organizations: This is a list of Internet organizations, or organizations that play or played a key role in the evolution of the Internet by developing recommendations, standards, and technology; deploying infrastructure and services; and addressing other major issues.Aureusidin synthase: Aureusidin synthase (, AmAS1) is an enzyme with system name 2',4,4',6'-tetrahydroxychalcone 4'-O-beta-D-glucoside:oxygen oxidoreductase.Wheat middlings: Wheat middlings (also known as millfeed, wheat mill run, or wheat midds) is the middle of three grades into which flour and meal are classified: patents, middlings, and clears. Middlings are often used in animal feed.De novo transcriptome assembly: De novo transcriptome assembly is the method of creating a transcriptome without the aid of a reference genome.Thermal cyclerImmersive technologyFungicide use in the United States: A more accurate title for this page would be "Common plant pathogens to food crops in the United States".WGAViewer: WGAViewer is a bioinformatics software tool which is designed to visualize, annotate, and help interpret the results generated from a genome wide association study (GWAS). Alongside the P values of association, WGAViewer allows a researcher to visualize and consider other supporting evidence, such as the genomic context of the SNP, linkage disequilibrium (LD) with ungenotyped SNPs, gene expression database, and the evidence from other GWAS projects, when determining the potential importance of an individual SNP.Eukaryotic transcription: Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells.Endodermis: The endodermis is the central, innermost layer of cortex in some land plants. It is made of compact living cells surrounded by an outer ring of endodermal cells that are impregnated with hydrophobic substances (Casparian Strip) to restrict apoplastic flow of water to the inside.Pediatric ophthalmology: Pediatric ophthalmology is a sub-speciality of ophthalmology concerned with eye diseases, visual development, and vision care in children.Southern corn leaf blight: Southern corn leaf blight (SCLB) is a fungal disease of maize caused by the plant pathogen Bipolaris maydis (also known as Cochliobolus heterostrophus in its teleomorph state).Lentil: The lentil (Lens culinaris) is an edible pulse. It is a bushy annual plant of the legume family, known for its lens-shaped seeds.Water supply in Miyakojima: The water supply in Miyakojima involves the history and development of the current water supply in Miyakojima, a small coral island with only one river, which is administered by Okinawa Prefecture, in Japan.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Coffea: Coffea is a genus of flowering plants whose seeds, called coffee beans, are used to make coffee. It is a member of the family Rubiaceae.Sweet sorghumAlternative splicing: Alternative splicing is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.Brunfelsia: Brunfelsia is a genus of flowering plants in the family Solanaceae, the nightshades. There are about 50 species described.Protein subcellular localization prediction: Protein subcellular localization prediction (or just protein localization prediction) involves the computational prediction of where a protein resides in a cell.Leifsonia xyli xyli: Leifsonia xyli subsp. xyli is a small, fastidious, Gram-positive, coryneform bacterium that causes ratoon stunting disease, a major worldwide disease of sugarcane.Intron: right|thumbnail|270px|Representation of intron and [[exons within a simple gene containing a single intron.]]Fragaria × vescana: Fragaria × vescana is a hybrid strawberry cultivar that was created in an effort to combine the best traits of the garden strawberry (Fragaria × ananassa), which has large berries and vigorous plants, with the woodland strawberry (Fragaria vesca), which has an exquisite flavour, but small berries.Heterodera schachtii: Heterodera schachtii Heterodera schactii at Nemaplex, University of CaliforniaHeterodera schactii at Knowledge Master (Beet cyst eelworm, Sugarbeet nematode) is a plant pathogenic nematode. It infects more than 200 different plants including economically important crops such as sugar beets, cabbage, broccoli, and radish.Massive parallel sequencing: Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation sequencing. Some of these technologies emerged in 1994-1998 and became commercially available since 2005.Mycelium Running: Mycelium Running: How Mushrooms Can Help Save the World is the sixth book written by American mycologist Paul Stamets.Cyanidioschyzon merolae: C. merolae is a small (2μm), club-shaped, unicellular haploid red alga adapted to high sulfur acidic hot spring environments (pH 1.Canna Leaf Roller: Cannas are largely free of pests, but in the USA plants sometimes fall victim the Canna Leaf Roller, which can actually be two different insects. Larva of the Brazilian skipper butterfly (Calpodes ethlius), also known as the Larger Canna Leaf Roller, cut the leaves and roll them over to live inside while pupating and eating the leaf.Phacidiopycnis padwickii: Phacidiopycnis padwickii is a plant pathogen infecting chickpea.Amelanchier alnifolia: Amelanchier alnifolia, the saskatoon, Pacific serviceberry, western serviceberry, alder-leaf shadbush, dwarf shadbush, chuckley pear, or western juneberry,Germplasm Resources Information Network: Amelanchier alnifolia is a shrub with edible berry-like fruit, native to North America from Alaska across most of western Canada and in the western and north-central United States. Historically, it was also called pigeon berry.Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Tomato seed oil: Tomato seed oil is a vegetable oil extracted from the seeds of tomatoes.Flower box: __NOTOC__

(1/3795) Mining SNPs from EST databases.

There is considerable interest in the discovery and characterization of single nucleotide polymorphisms (SNPs) to enable the analysis of the potential relationships between human genotype and phenotype. Here we present a strategy that permits the rapid discovery of SNPs from publicly available expressed sequence tag (EST) databases. From a set of ESTs derived from 19 different cDNA libraries, we assembled 300,000 distinct sequences and identified 850 mismatches from contiguous EST data sets (candidate SNP sites), without de novo sequencing. Through a polymerase-mediated, single-base, primer extension technique, Genetic Bit Analysis (GBA), we confirmed the presence of a subset of these candidate SNP sites and have estimated the allele frequencies in three human populations with different ethnic origins. Altogether, our approach provides a basis for rapid and efficient regional and genome-wide SNP discovery using data assembled from sequences from different libraries of cDNAs.  (+info)

(2/3795) UCP4, a novel brain-specific mitochondrial protein that reduces membrane potential in mammalian cells.

Uncoupling proteins (UCPs) are a family of mitochondrial transporter proteins that have been implicated in thermoregulatory heat production and maintenance of the basal metabolic rate. We have identified and partially characterized a novel member of the human uncoupling protein family, termed uncoupling protein-4 (UCP4). Protein sequence analyses showed that UCP4 is most related to UCP3 and possesses features characteristic of mitochondrial transporter proteins. Unlike other known UCPs, UCP4 transcripts are exclusively expressed in both fetal and adult brain tissues. UCP4 maps to human chromosome 6p11.2-q12. Consistent with its potential role as an uncoupling protein, UCP4 is localized to the mitochondria and its ectopic expression in mammalian cells reduces mitochondrial membrane potential. These findings suggest that UCP4 may be involved in thermoregulatory heat production and metabolism in the brain.  (+info)

(3/3795) Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.  (+info)

(4/3795) The Dictyostelium developmental cDNA project: generation and analysis of expressed sequence tags from the first-finger stage of development.

In an effort to identify and characterize genes expressed during multicellular development ill Dictyostelium, we have undertaken a cDNA sequencing project. Using size-fractionated subsets of cDNA from the first finger stage, two sets of gridded libraries were constructed for cDNA sequencing. One, library S, consisting of 9984 clones, carries relatively short inserts, and the other, library L, which consists of 8448 clones, has longer inserts. We sequenced all the selected clones in library S from their 3'-ends, and this generated 3093 non-redundant, expressed sequence tags (ESTs). Among them, 246 ESTs hit known Dictyostelium genes and 910 showed significant similarity to genes of Dictyostelium and other organisms. For library L, 1132 clones were randomly sequenced and 471 non-redundant ESTs were obtained. In combination, the ESTs from the two libraries represent approximately 40% of genes expressed in late development, assuming that the non-redundant ESTs correspond to independent genes. They will provide a useful resource for investigating the genetic networks that regulate multicellular development of this organism.  (+info)

(5/3795) Molecular identification of human G-substrate, a possible downstream component of the cGMP-dependent protein kinase cascade in cerebellar Purkinje cells.

G-substrate, an endogenous substrate for cGMP-dependent protein kinase, exists almost exclusively in cerebellar Purkinje cells, where it is possibly involved in the induction of long-term depression. A G-substrate cDNA was identified by screening expressed sequence tag databases from a human brain library. The deduced amino acid sequence of human G-substrate contained two putative phosphorylation sites (Thr-68 and Thr-119) with amino acid sequences [KPRRKDT(p)PALH] that were identical to those reported for rabbit G-substrate. G-substrate mRNA was expressed almost exclusively in the cerebellum as a single transcript. The human G-substrate gene was mapped to human chromosome 7p15 by radiation hybrid panel analysis. In vitro translation products of the cDNA showed an apparent molecular mass of 24 kDa on SDS/PAGE which was close to that of purified rabbit G-substrate (23 kDa). Bacterially expressed human G-substrate is a heat-stable and acid-soluble protein that cross-reacts with antibodies raised against rabbit G-substrate. Recombinant human G-substrate was phosphorylated efficiently by cGMP-dependent protein kinase exclusively at Thr residues, and it was recognized by antibodies specific for rabbit phospho-G-substrate. The amino acid sequences surrounding the sites of phosphorylation in G-substrate are related to those around Thr-34 and Thr-35 of the dopamine- and cAMP-regulated phosphoprotein DARPP-32 and inhibitor-1, respectively, two potent inhibitors of protein phosphatase 1. However, purified G-substrate phosphorylated by cGMP-dependent protein kinase inhibited protein phosphatase 2A more effectively than protein phosphatase 1, suggesting a distinct role as a protein phosphatase inhibitor.  (+info)

(6/3795) Cloning, expression, and genetic mapping of Sema W, a member of the semaphorin family.

The semaphorins comprise a large family of membrane-bound and secreted proteins, some of which have been shown to function in axon guidance. We have cloned a transmembrane semaphorin, Sema W, that belongs to the class IV subgroup of the semaphorin family. The mouse and rat forms of Sema W show 97% amino acid sequence identity with each other, and each shows about 91% identity with the human form. The gene for Sema W is divided into 15 exons, up to 4 of which are absent in the human cDNAs that we sequenced. Unlike many other semaphorins, Sema W is expressed at low levels in the developing embryo but was found to be expressed at high levels in the adult central nervous system and lung. Functional studies with purified membrane fractions from COS7 cells transfected with a Sema W expression plasmid showed that Sema W has growth-cone collapse activity against retinal ganglion-cell axons, indicating that vertebrate transmembrane semaphorins, like secreted semaphorins, can collapse growth cones. Genetic mapping of human SEMAW with human/hamster radiation hybrids localized the gene to chromosome 2p13. Genetic mapping of mouse Semaw with mouse/hamster radiation hybrids localized the gene to chromosome 6, and physical mapping placed the gene on bacteria artificial chromosomes carrying microsatellite markers D6Mit70 and D6Mit189. This localization places Semaw within the locus for motor neuron degeneration 2, making it an attractive candidate gene for this disease.  (+info)

(7/3795) Exon shuffling by L1 retrotransposition.

Long interspersed nuclear elements (LINE-1s or L1s) are the most abundant retrotransposons in the human genome, and they serve as major sources of reverse transcriptase activity. Engineered L1s retrotranspose at high frequency in cultured human cells. Here it is shown that L1s insert into transcribed genes and retrotranspose sequences derived from their 3' flanks to new genomic locations. Thus, retrotransposition-competent L1s provide a vehicle to mobilize non-L1 sequences, such as exons or promoters, into existing genes and may represent a general mechanism for the evolution of new genes.  (+info)

(8/3795) A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases.

MOTIVATION: Word-matching algorithms such as BLAST are routinely used for sequence comparison. These algorithms typically use areas of matching words to seed alignments which are then used to assess the degree of sequence similarity. In this paper, we show that by formally separating the word-matching and sequence-alignment process, and using information about word frequencies to generate alignments and similarity scores, we can create a new sequence-comparison algorithm which is both fast and sensitive. The formal split between word searching and alignment allows users to select an appropriate alignment method without affecting the underlying similarity search. The algorithm has been used to develop software for identifying entries in DNA sequence databases which are contaminated with vector sequence. RESULTS: We present three algorithms, RAPID, PHAT and SPLAT, which together allow vector contaminations to be found and assessed extremely rapidly. RAPID is a word search algorithm which uses probabilities to modify the significance attached to different words; PHAT and SPLAT are alignment algorithms. An initial implementation has been shown to be approximately an order of magnitude faster than BLAST. The formal split between word searching and alignment not only offers considerable gains in performance, but also allows alignment generation to be viewed as a user interface problem, allowing the most useful output method to be selected without affecting the underlying similarity search. Receiver Operator Characteristic (ROC) analysis of an artificial test set allows the optimal score threshold for identifying vector contamination to be determined. ROC curves were also used to determine the optimum word size (nine) for finding vector contamination. An analysis of the entire expressed sequence tag (EST) subset of EMBL found a contamination rate of 0.27%. A more detailed analysis of the 50 000 ESTs in est10.dat (an EST subset of EMBL) finds an error rate of 0.86%, principally due to two large-scale projects. AVAILABILITY: A Web page for the software exists at http://bioinf.man.ac.uk/rapid, or it can be downloaded from ftp://ftp.bioinf.man.ac.uk/RAPID CONTACT: crispin@cs.man.ac.uk  (+info)



ESTs


  • Expressed Sequence Tags (ESTs) are a technology used to explore the transcriptome (a record of this gene activity). (journals.co.za)
  • In this study, 4847 expressed sequenced tags (ESTs) from mixed stages of the migratory plant-parasitic nematode Ditylenchus africanus (peanut pod nematode) were investigated. (edu.mk)
  • Furthermore, seven putative novel candidate parasitism genes were identified based on the prediction of a signal peptide in the corresponding protein sequence and homologous ESTs exclusively in parasitic nematodes. (edu.mk)
  • Expressed sequence tags (ESTs) have proven useful for gene discovery in many crops. (sciencesocieties.org)
  • A bioinformatics package to analyse ESTs (Expressed Sequence Tags) easily. (brothersoft.com)

differentially


  • Using modifications of a previously documented technique, the differential display polymerase chain reaction, we describe the isolation of differentially expressed sequence tags, short complementary DNA fragments corresponding to mRNAs that are differentially expressed in breast cancer biopsies, as compared to normal breast tissue controls. (aacrjournals.org)
  • Differentially displayed expressed sequence tags in Melipona scutellaris (Hymenoptera, Apidae, Meliponini) development. (scielo.br)

Sequencing


  • Direct sequencing and expression analysis of two sequence tags demonstrate that they represent sequences which are overexpressed in a number of breast carcinoma cell lines. (aacrjournals.org)
  • Comparisons with previous root EST sequencing and between the two libraries made here resulted in a set of genes to study further for differential gene expression and adaptation to low P, such as a 14 kDa praline-rich protein, a metallopeptidase, tonoplast intrinsic protein, adenosine triphosphate (ATP) citrate synthase, and cell proliferation genes expressed in the low P treated plants. (sciencesocieties.org)
  • Large numbers of cDNA libraries have been constructed for several crops with minimal sequencing of each library to determine the genes expressed in each of many different tissues. (sciencesocieties.org)

sequences


  • Among the unique sequences, 62.7% encoded putative proteins that shared significant sequence similarities (E-value ≤ 10 -3 )with the sequences available in GenBank. (pubmedcentralcanada.ca)
  • Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)

genes


  • Knowledge of the genes that are expressed in the insect gut are crucial for understanding basic physiology of food digestion, their interactions with Bacillus thuringiensis (Bt) toxins, and for discovering new targets for novel toxins for use in pest management. (pubmedcentralcanada.ca)
  • Other tags showed homology to genes previously described as being involved in parasitism (expansin, SEC-2, calreticulin, 14-3-3b and various allergen proteins). (edu.mk)
  • Expressed sequence tag analysis of 3648 clones identified 2372 unigenes, of which 1591 were annotated as known genes while a total of 465 unigenes were not associated with any known gene. (sciencesocieties.org)
  • Given the young tissue used to make the root libraries, genes for catalytic activity and binding were highly expressed. (sciencesocieties.org)
  • Expressed sequence tags are considered to be part of the transcriptome and to represent to a greater or lesser degree the genes expressed in the genotypes and tissues at the time point at which the mRNA was extracted. (sciencesocieties.org)

alignment


  • Is the Subject Area "Sequence alignment" applicable to this article? (plos.org)

libraries


  • Only a few studies have focused on developing expressed sequence tag (EST) libraries from the guts of lepidopteran larvae. (pubmedcentralcanada.ca)