DroSpeGe: rapid access database for new Drosophila species genomes
Identifieur interne : 000F13 ( Main/Exploration ); précédent : 000F12; suivant : 000F14DroSpeGe: rapid access database for new Drosophila species genomes
Auteurs : Donald G. Gilbert [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2007-01.
English descriptors
- KwdEn :
- MESH :
- classification : Drosophila.
- genetics : Drosophila.
- Animals, Chromosome Mapping, Chromosomes, Databases, Genetic, Genetic Variation, Genome, Insect, Genomics, Internet, Software, User-Computer Interface.
Abstract
The Drosophila species comparative genome database DroSpeGe () provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.
Url:
- https://api.istex.fr/document/B59A1BEB836EE57059BA425A5291C43704A9C556/fulltext/pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899099
DOI: 10.1093/nar/gkl997
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 000115
- to stream Istex, to step Curation: 000115
- to stream Istex, to step Checkpoint: 000576
- to stream Pmc, to step Corpus: 000571
- to stream Pmc, to step Curation: 000571
- to stream Pmc, to step Checkpoint: 000697
- to stream PubMed, to step Corpus: 000084
- to stream PubMed, to step Curation: 000084
- to stream PubMed, to step Checkpoint: 000084
- to stream Ncbi, to step Merge: 000018
- to stream Ncbi, to step Curation: 000018
- to stream Ncbi, to step Checkpoint: 000018
- to stream Main, to step Merge: 000F20
- to stream Main, to step Curation: 000F13
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title>DroSpeGe: rapid access database for new Drosophila species genomes</title><author wicri:is="90%"><name sortKey="Gilbert, Donald G" sort="Gilbert, Donald G" uniqKey="Gilbert D" first="Donald G." last="Gilbert">Donald G. Gilbert</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:B59A1BEB836EE57059BA425A5291C43704A9C556</idno><date when="2007" year="2007">2007</date><idno type="doi">10.1093/nar/gkl997</idno><idno type="url">https://api.istex.fr/document/B59A1BEB836EE57059BA425A5291C43704A9C556/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000115</idno><idno type="wicri:Area/Istex/Curation">000115</idno><idno type="wicri:Area/Istex/Checkpoint">000576</idno><idno type="wicri:doubleKey">0305-1048:2007:Gilbert D:drospege:rapid:access</idno><idno type="wicri:source">PMC</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899099</idno><idno type="RBID">PMC:1899099</idno><idno type="wicri:Area/Pmc/Corpus">000571</idno><idno type="wicri:Area/Pmc/Curation">000571</idno><idno type="wicri:Area/Pmc/Checkpoint">000697</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000084</idno><idno type="wicri:Area/PubMed/Curation">000084</idno><idno type="wicri:Area/PubMed/Checkpoint">000084</idno><idno type="wicri:Area/Ncbi/Merge">000018</idno><idno type="wicri:Area/Ncbi/Curation">000018</idno><idno type="wicri:Area/Ncbi/Checkpoint">000018</idno><idno type="wicri:doubleKey">0305-1048:2007:Gilbert D:drospege:rapid:access</idno><idno type="wicri:Area/Main/Merge">000F20</idno><idno type="wicri:Area/Main/Curation">000F13</idno><idno type="wicri:Area/Main/Exploration">000F13</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a">DroSpeGe: rapid access database for new Drosophila species genomes</title><author wicri:is="90%"><name sortKey="Gilbert, Donald G" sort="Gilbert, Donald G" uniqKey="Gilbert D" first="Donald G." last="Gilbert">Donald G. Gilbert</name><affiliation wicri:level="2"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Indiana University, Bloomington, IN 47405</wicri:regionArea><placeName><region type="state">Indiana</region></placeName></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author></analytic><monogr></monogr><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2007-01">2007-01</date><biblScope unit="volume">35</biblScope><biblScope unit="supplement">suppl_1</biblScope><biblScope unit="page" from="D480">D480</biblScope><biblScope unit="page" to="D485">D485</biblScope></imprint><idno type="ISSN">0305-1048</idno></series><idno type="istex">B59A1BEB836EE57059BA425A5291C43704A9C556</idno><idno type="DOI">10.1093/nar/gkl997</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Chromosome Mapping</term><term>Chromosomes</term><term>Databases, Genetic</term><term>Drosophila (classification)</term><term>Drosophila (genetics)</term><term>Genetic Variation</term><term>Genome, Insect</term><term>Genomics</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Drosophila</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drosophila</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Chromosome Mapping</term><term>Chromosomes</term><term>Databases, Genetic</term><term>Genetic Variation</term><term>Genome, Insect</term><term>Genomics</term><term>Internet</term><term>Software</term><term>User-Computer Interface</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">The Drosophila species comparative genome database DroSpeGe () provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Indiana</li></region></list><tree><country name="États-Unis"><region name="Indiana"><name sortKey="Gilbert, Donald G" sort="Gilbert, Donald G" uniqKey="Gilbert D" first="Donald G." last="Gilbert">Donald G. Gilbert</name></region><name sortKey="Gilbert, Donald G" sort="Gilbert, Donald G" uniqKey="Gilbert D" first="Donald G." last="Gilbert">Donald G. Gilbert</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000F13 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000F13 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Ticri/CIDE
|area= CyberinfraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:B59A1BEB836EE57059BA425A5291C43704A9C556
|texte= DroSpeGe: rapid access database for new Drosophila species genomes
}}
| This area was generated with Dilib version V0.6.25. |  |