openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
Identifieur interne : 002763 ( Main/Exploration ); précédent : 002762; suivant : 002764openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
Auteurs : Stephen Rudd [Finlande]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2005-01-01.
Abstract
The public expressed sequence tag collections are continually being enriched with high-quality sequences that represent an ever-expanding range of taxonomically diverse plant species. While these sequence collections provide biased insight into the populations of expressed genes available within individual species and their associated tissues, the information is conceivably of wider relevance in a comparative context. When we consider the available expressed sequence tag (EST) collections of summer 2004, most of the major plant taxonomic clades are at least superficially represented. Investigation of the five million available plant ESTs provides a wealth of information that has applications in modelling the routes of plant genome evolution and the identification of lineage-specific genes and gene families. Over four million ESTs from over 50 distinct plant species have been collated within an EST analysis pipeline called openSputnik. The ESTs were resolved down into approximately one million unigene sequences. These have been annotated using orthology-based annotation transfer from reference plant genomes and using a variety of contemporary bioinformatics methods to assign peptide, structural and functional attributes. The openSputnik database is available at http://sputnik.btk.fi.
Url:
DOI: 10.1093/nar/gki040
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 001104
- to stream Istex, to step Curation: 001104
- to stream Istex, to step Checkpoint: 000749
- to stream Main, to step Merge: 002881
- to stream Main, to step Curation: 002763
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections</title><author wicri:is="90%"><name sortKey="Rudd, Stephen" sort="Rudd, Stephen" uniqKey="Rudd S" first="Stephen" last="Rudd">Stephen Rudd</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:F8442B5116EB94F889E724B61A61EEB008CE8DAA</idno><date when="2005" year="2005">2005</date><idno type="doi">10.1093/nar/gki040</idno><idno type="url">https://api.istex.fr/document/F8442B5116EB94F889E724B61A61EEB008CE8DAA/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">001104</idno><idno type="wicri:Area/Istex/Curation">001104</idno><idno type="wicri:Area/Istex/Checkpoint">000749</idno><idno type="wicri:doubleKey">0305-1048:2005:Rudd S:opensputnik:a:database</idno><idno type="wicri:Area/Main/Merge">002881</idno><idno type="wicri:Area/Main/Curation">002763</idno><idno type="wicri:Area/Main/Exploration">002763</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections</title><author wicri:is="90%"><name sortKey="Rudd, Stephen" sort="Rudd, Stephen" uniqKey="Rudd S" first="Stephen" last="Rudd">Stephen Rudd</name><affiliation wicri:level="1"><country xml:lang="fr">Finlande</country><wicri:regionArea>Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku</wicri:regionArea><wicri:noRegion>FIN-20521 Turku</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2005-01-01">2005-01-01</date><biblScope unit="volume">33</biblScope><biblScope unit="supplement">suppl_1</biblScope><biblScope unit="page" from="D622">D622</biblScope><biblScope unit="page" to="D627">D627</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">F8442B5116EB94F889E724B61A61EEB008CE8DAA</idno><idno type="DOI">10.1093/nar/gki040</idno><idno type="local">gki040</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The public expressed sequence tag collections are continually being enriched with high-quality sequences that represent an ever-expanding range of taxonomically diverse plant species. While these sequence collections provide biased insight into the populations of expressed genes available within individual species and their associated tissues, the information is conceivably of wider relevance in a comparative context. When we consider the available expressed sequence tag (EST) collections of summer 2004, most of the major plant taxonomic clades are at least superficially represented. Investigation of the five million available plant ESTs provides a wealth of information that has applications in modelling the routes of plant genome evolution and the identification of lineage-specific genes and gene families. Over four million ESTs from over 50 distinct plant species have been collated within an EST analysis pipeline called openSputnik. The ESTs were resolved down into approximately one million unigene sequences. These have been annotated using orthology-based annotation transfer from reference plant genomes and using a variety of contemporary bioinformatics methods to assign peptide, structural and functional attributes. The openSputnik database is available at http://sputnik.btk.fi.</div></front></TEI><affiliations><list><country><li>Finlande</li></country></list><tree><country name="Finlande"><noRegion><name sortKey="Rudd, Stephen" sort="Rudd, Stephen" uniqKey="Rudd S" first="Stephen" last="Rudd">Stephen Rudd</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002763 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002763 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:F8442B5116EB94F889E724B61A61EEB008CE8DAA
|texte= openSputnik—a database to ESTablish comparative plant genomics using unsaturated sequence collections
}}
| This area was generated with Dilib version V0.6.25. |  |