SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.
Identifieur interne : 000007 ( PubMed/Checkpoint ); précédent : 000006; suivant : 000008SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.
Auteurs : Haibao Tang ; Matthew D. Bomhoff ; Evan Briones ; Liangsheng Zhang [République populaire de Chine] ; James C. Schnable ; Eric Lyons [Oman]Source :
- Genome biology and evolution [ 1759-6653 ] ; 2015.
Abstract
The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition. However, the identification of syntenic regions requires complex analyses which must be repeated for pairwise comparisons between any two species. Therefore, as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes. SynFind is capable of reporting per-gene information, useful for researchers studying specific gene families, as well as genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.
DOI: 10.1093/gbe/evv219
PubMed: 26560340
Affiliations:
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Bomhoff</name><affiliation><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</nlm:affiliation><wicri:noCountry code="subField">University of Arizona</wicri:noCountry></affiliation></author><author><name sortKey="Briones, Evan" sort="Briones, Evan" uniqKey="Briones E" first="Evan" last="Briones">Evan Briones</name><affiliation><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</nlm:affiliation><wicri:noCountry code="subField">University of Arizona</wicri:noCountry></affiliation></author><author><name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province</wicri:regionArea><wicri:noRegion>Fujian Province</wicri:noRegion></affiliation></author><author><name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C" last="Schnable">James C. Schnable</name><affiliation><nlm:affiliation>Department of Agronomy and Horticulture, University of Nebraska, Lincoln.</nlm:affiliation><wicri:noCountry code="subField">Lincoln</wicri:noCountry></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona elyons.uoa@gmail.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>School of Plant Sciences, iPlant Collaborative</wicri:regionArea><wicri:noRegion>iPlant Collaborative</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:26560340</idno><idno type="pmid">26560340</idno><idno type="doi">10.1093/gbe/evv219</idno><idno type="wicri:Area/PubMed/Corpus">000006</idno><idno type="wicri:Area/PubMed/Curation">000006</idno><idno type="wicri:Area/PubMed/Checkpoint">000006</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.</title><author><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name><affiliation><nlm:affiliation>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona.</nlm:affiliation><wicri:noCountry code="subField">University of Arizona</wicri:noCountry></affiliation></author><author><name sortKey="Bomhoff, Matthew D" sort="Bomhoff, Matthew D" uniqKey="Bomhoff M" first="Matthew D" last="Bomhoff">Matthew D. Bomhoff</name><affiliation><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</nlm:affiliation><wicri:noCountry code="subField">University of Arizona</wicri:noCountry></affiliation></author><author><name sortKey="Briones, Evan" sort="Briones, Evan" uniqKey="Briones E" first="Evan" last="Briones">Evan Briones</name><affiliation><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</nlm:affiliation><wicri:noCountry code="subField">University of Arizona</wicri:noCountry></affiliation></author><author><name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province</wicri:regionArea><wicri:noRegion>Fujian Province</wicri:noRegion></affiliation></author><author><name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C" last="Schnable">James C. Schnable</name><affiliation><nlm:affiliation>Department of Agronomy and Horticulture, University of Nebraska, Lincoln.</nlm:affiliation><wicri:noCountry code="subField">Lincoln</wicri:noCountry></affiliation></author><author><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name><affiliation wicri:level="1"><nlm:affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona elyons.uoa@gmail.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>School of Plant Sciences, iPlant Collaborative</wicri:regionArea><wicri:noRegion>iPlant Collaborative</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition. However, the identification of syntenic regions requires complex analyses which must be repeated for pairwise comparisons between any two species. Therefore, as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes. SynFind is capable of reporting per-gene information, useful for researchers studying specific gene families, as well as genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.</div></front></TEI><pubmed><MedlineCitation Owner="NLM" Status="In-Process"><PMID Version="1">26560340</PMID><DateCreated><Year>2015</Year><Month>12</Month><Day>28</Day></DateCreated><DateRevised><Year>2016</Year><Month>01</Month><Day>07</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>12</Issue><PubDate><Year>2015</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.</ArticleTitle><Pagination><MedlinePgn>3286-98</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evv219</ELocationID><Abstract><AbstractText>The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition. However, the identification of syntenic regions requires complex analyses which must be repeated for pairwise comparisons between any two species. Therefore, as the number of published genomes increases, there is a growing demand for scalable, simple-to-use applications to perform comparative genomic analyses that cater to both gene family studies and genome-scale studies. We implemented SynFind, a web-based tool that addresses this need. Given one query genome, SynFind is capable of identifying conserved syntenic regions in any set of target genomes. SynFind is capable of reporting per-gene information, useful for researchers studying specific gene families, as well as genome-wide data sets of syntenic gene and predicted gene locations, critical for researchers focused on large-scale genomic analyses. Inference of syntenic homologs provides the basis for correlation of functional changes around genes of interests between related organisms. Deployed on the CoGe online platform, SynFind is connected to the genomic data from over 15,000 organisms from all domains of life as well as supporting multiple releases of the same organism. SynFind makes use of a powerful job execution framework that promises scalability and reproducibility. SynFind can be accessed at http://genomevolution.org/CoGe/SynFind.pl. A video tutorial of SynFind using Phytophthrora as an example is available at http://www.youtube.com/watch?v=2Agczny9Nyc.</AbstractText><CopyrightInformation>© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Haibao</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bomhoff</LastName><ForeName>Matthew D</ForeName><Initials>MD</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Briones</LastName><ForeName>Evan</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Liangsheng</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schnable</LastName><ForeName>James C</ForeName><Initials>JC</Initials><AffiliationInfo><Affiliation>Department of Agronomy and Horticulture, University of Nebraska, Lincoln.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lyons</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>School of Plant Sciences, iPlant Collaborative, University of Arizona elyons.uoa@gmail.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList 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27;102(39):13950-5</RefSource><PMID Version="1">16172379</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2005 Oct;15(10):1456-61</RefSource><PMID Version="1">16169922</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2007 Dec;17(12):1837-49</RefSource><PMID Version="1">17989258</PMID></CommentsCorrections></CommentsCorrectionsList><OtherID Source="NLM">PMC4700967</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">cyberinfrastructure</Keyword><Keyword MajorTopicYN="N">genome evolution</Keyword><Keyword MajorTopicYN="N">homology</Keyword><Keyword MajorTopicYN="N">synteny</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>11</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>11</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>11</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26560340</ArticleId><ArticleId IdType="pii">evv219</ArticleId><ArticleId IdType="doi">10.1093/gbe/evv219</ArticleId><ArticleId IdType="pmc">PMC4700967</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Oman</li><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Bomhoff, Matthew D" sort="Bomhoff, Matthew D" uniqKey="Bomhoff M" first="Matthew D" last="Bomhoff">Matthew D. Bomhoff</name><name sortKey="Briones, Evan" sort="Briones, Evan" uniqKey="Briones E" first="Evan" last="Briones">Evan Briones</name><name sortKey="Schnable, James C" sort="Schnable, James C" uniqKey="Schnable J" first="James C" last="Schnable">James C. Schnable</name><name sortKey="Tang, Haibao" sort="Tang, Haibao" uniqKey="Tang H" first="Haibao" last="Tang">Haibao Tang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Zhang, Liangsheng" sort="Zhang, Liangsheng" uniqKey="Zhang L" first="Liangsheng" last="Zhang">Liangsheng Zhang</name></noRegion></country><country name="Oman"><noRegion><name sortKey="Lyons, Eric" sort="Lyons, Eric" uniqKey="Lyons E" first="Eric" last="Lyons">Eric Lyons</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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