OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
Identifieur interne : 003D61 ( Main/Exploration ); précédent : 003D60; suivant : 003D62OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
Auteurs : Joanna C. Chiu [États-Unis] ; Ernest K. Lee ; Mary G. Egan ; Indra Neil Sarkar ; Gloria M. Coruzzi ; Rob DesalleSource :
- Bioinformatics (Oxford, England) [ 1367-4803 ] ; 2006.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Alignement de séquences (méthodes), Analyse de séquence d'ADN (méthodes), Bases de données génétiques (MeSH), Cartographie chromosomique (méthodes), Intelligence artificielle (MeSH), Interface utilisateur (MeSH), Logiciel (MeSH), Phylogenèse (MeSH), Reconnaissance automatique des formes (méthodes), Similitude de séquences d'acides nucléiques (MeSH), Séquence conservée (génétique).
- MESH :
- génétique : Séquence conservée.
- méthodes : Alignement de séquences, Analyse de séquence d'ADN, Cartographie chromosomique, Reconnaissance automatique des formes.
- Algorithmes, Bases de données génétiques, Intelligence artificielle, Interface utilisateur, Logiciel, Phylogenèse, Similitude de séquences d'acides nucléiques.
English descriptors
- KwdEn :
- Algorithms (MeSH), Artificial Intelligence (MeSH), Chromosome Mapping (methods), Conserved Sequence (genetics), Databases, Genetic (MeSH), Pattern Recognition, Automated (methods), Phylogeny (MeSH), Sequence Alignment (methods), Sequence Analysis, DNA (methods), Sequence Homology, Nucleic Acid (MeSH), Software (MeSH), User-Computer Interface (MeSH).
- MESH :
Abstract
MOTIVATION
The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.
RESULTS
We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.
AVAILABILITY
http://nypg.bio.nyu.edu/orthologid/
DOI: 10.1093/bioinformatics/btk040
PubMed: 16410324
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Egan</name></author><author><name sortKey="Sarkar, Indra Neil" sort="Sarkar, Indra Neil" uniqKey="Sarkar I" first="Indra Neil" last="Sarkar">Indra Neil Sarkar</name></author><author><name sortKey="Coruzzi, Gloria M" sort="Coruzzi, Gloria M" uniqKey="Coruzzi G" first="Gloria M" last="Coruzzi">Gloria M. Coruzzi</name></author><author><name sortKey="Desalle, Rob" sort="Desalle, Rob" uniqKey="Desalle R" first="Rob" last="Desalle">Rob Desalle</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16410324</idno><idno type="pmid">16410324</idno><idno type="doi">10.1093/bioinformatics/btk040</idno><idno type="wicri:Area/Main/Corpus">003E93</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003E93</idno><idno type="wicri:Area/Main/Curation">003E93</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">003E93</idno><idno type="wicri:Area/Main/Exploration">003E93</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">OrthologID: automation of genome-scale ortholog identification within a parsimony framework.</title><author><name sortKey="Chiu, Joanna C" sort="Chiu, Joanna C" uniqKey="Chiu J" first="Joanna C" last="Chiu">Joanna C. Chiu</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, New York University, New York, NY 10003, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, New York University, New York, NY 10003</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Lee, Ernest K" sort="Lee, Ernest K" uniqKey="Lee E" first="Ernest K" last="Lee">Ernest K. Lee</name></author><author><name sortKey="Egan, Mary G" sort="Egan, Mary G" uniqKey="Egan M" first="Mary G" last="Egan">Mary G. Egan</name></author><author><name sortKey="Sarkar, Indra Neil" sort="Sarkar, Indra Neil" uniqKey="Sarkar I" first="Indra Neil" last="Sarkar">Indra Neil Sarkar</name></author><author><name sortKey="Coruzzi, Gloria M" sort="Coruzzi, Gloria M" uniqKey="Coruzzi G" first="Gloria M" last="Coruzzi">Gloria M. Coruzzi</name></author><author><name sortKey="Desalle, Rob" sort="Desalle, Rob" uniqKey="Desalle R" first="Rob" last="Desalle">Rob Desalle</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="ISSN">1367-4803</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Artificial Intelligence (MeSH)</term><term>Chromosome Mapping (methods)</term><term>Conserved Sequence (genetics)</term><term>Databases, Genetic (MeSH)</term><term>Pattern Recognition, Automated (methods)</term><term>Phylogeny (MeSH)</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Sequence Homology, Nucleic Acid (MeSH)</term><term>Software (MeSH)</term><term>User-Computer Interface (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes (MeSH)</term><term>Alignement de séquences (méthodes)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Bases de données génétiques (MeSH)</term><term>Cartographie chromosomique (méthodes)</term><term>Intelligence artificielle (MeSH)</term><term>Interface utilisateur (MeSH)</term><term>Logiciel (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Reconnaissance automatique des formes (méthodes)</term><term>Similitude de séquences d'acides nucléiques (MeSH)</term><term>Séquence conservée (génétique)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Conserved Sequence</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Séquence conservée</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term><term>Pattern Recognition, Automated</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Cartographie chromosomique</term><term>Reconnaissance automatique des formes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Artificial Intelligence</term><term>Databases, Genetic</term><term>Phylogeny</term><term>Sequence Homology, Nucleic Acid</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Bases de données génétiques</term><term>Intelligence artificielle</term><term>Interface utilisateur</term><term>Logiciel</term><term>Phylogenèse</term><term>Similitude de séquences d'acides nucléiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>MOTIVATION</b></p><p>The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes.</p></div><div type="abstract" xml:lang="en"><p><b>AVAILABILITY</b></p><p>http://nypg.bio.nyu.edu/orthologid/</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16410324</PMID><DateCompleted><Year>2006</Year><Month>05</Month><Day>10</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1367-4803</ISSN><JournalIssue CitedMedium="Print"><Volume>22</Volume><Issue>6</Issue><PubDate><Year>2006</Year><Month>Mar</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>OrthologID: automation of genome-scale ortholog identification within a parsimony framework.</ArticleTitle><Pagination><MedlinePgn>699-707</MedlinePgn></Pagination><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. 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Coruzzi</name><name sortKey="Desalle, Rob" sort="Desalle, Rob" uniqKey="Desalle R" first="Rob" last="Desalle">Rob Desalle</name><name sortKey="Egan, Mary G" sort="Egan, Mary G" uniqKey="Egan M" first="Mary G" last="Egan">Mary G. Egan</name><name sortKey="Lee, Ernest K" sort="Lee, Ernest K" uniqKey="Lee E" first="Ernest K" last="Lee">Ernest K. Lee</name><name sortKey="Sarkar, Indra Neil" sort="Sarkar, Indra Neil" uniqKey="Sarkar I" first="Indra Neil" last="Sarkar">Indra Neil Sarkar</name></noCountry><country name="États-Unis"><region name="État de New York"><name sortKey="Chiu, Joanna C" sort="Chiu, Joanna C" uniqKey="Chiu J" first="Joanna C" last="Chiu">Joanna C. Chiu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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