JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
Identifieur interne : 000D66 ( Main/Exploration ); précédent : 000D65; suivant : 000D67JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
Auteurs : Michael Richter [Allemagne] ; Thierry Lombardot [Allemagne] ; Ivaylo Kostadinov [Allemagne] ; Renzo Kottmann [Allemagne] ; Melissa Beth Duhaime [Allemagne] ; Jörg Peplies [Allemagne] ; Frank Oliver Glöckner [Allemagne]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2008.
Abstract
Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.
The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets.
JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.
Url:
DOI: 10.1186/1471-2105-9-177
PubMed: 18380896
PubMed Central: 2311307
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000198
- to stream Pmc, to step Curation: 000198
- to stream Pmc, to step Checkpoint: 000670
- to stream Ncbi, to step Merge: 000044
- to stream Ncbi, to step Curation: 000044
- to stream Ncbi, to step Checkpoint: 000044
- to stream Main, to step Merge: 000D73
- to stream Main, to step Curation: 000D66
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes</title><author><name sortKey="Richter, Michael" sort="Richter, Michael" uniqKey="Richter M" first="Michael" last="Richter">Michael Richter</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Lombardot, Thierry" sort="Lombardot, Thierry" uniqKey="Lombardot T" first="Thierry" last="Lombardot">Thierry Lombardot</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Kottmann, Renzo" sort="Kottmann, Renzo" uniqKey="Kottmann R" first="Renzo" last="Kottmann">Renzo Kottmann</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Duhaime, Melissa Beth" sort="Duhaime, Melissa Beth" uniqKey="Duhaime M" first="Melissa Beth" last="Duhaime">Melissa Beth Duhaime</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Peplies, Jorg" sort="Peplies, Jorg" uniqKey="Peplies J" first="Jörg" last="Peplies">Jörg Peplies</name><affiliation wicri:level="1"><nlm:aff id="I3">Ribocon GmbH D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Ribocon GmbH D-28359 Bremen</wicri:regionArea></affiliation></author><author><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18380896</idno><idno type="pmc">2311307</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2311307</idno><idno type="RBID">PMC:2311307</idno><idno type="doi">10.1186/1471-2105-9-177</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000198</idno><idno type="wicri:Area/Pmc/Curation">000198</idno><idno type="wicri:Area/Pmc/Checkpoint">000670</idno><idno type="wicri:Area/Ncbi/Merge">000044</idno><idno type="wicri:Area/Ncbi/Curation">000044</idno><idno type="wicri:Area/Ncbi/Checkpoint">000044</idno><idno type="wicri:Area/Main/Merge">000D73</idno><idno type="wicri:Area/Main/Curation">000D66</idno><idno type="wicri:Area/Main/Exploration">000D66</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes</title><author><name sortKey="Richter, Michael" sort="Richter, Michael" uniqKey="Richter M" first="Michael" last="Richter">Michael Richter</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Lombardot, Thierry" sort="Lombardot, Thierry" uniqKey="Lombardot T" first="Thierry" last="Lombardot">Thierry Lombardot</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Kottmann, Renzo" sort="Kottmann, Renzo" uniqKey="Kottmann R" first="Renzo" last="Kottmann">Renzo Kottmann</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Duhaime, Melissa Beth" sort="Duhaime, Melissa Beth" uniqKey="Duhaime M" first="Melissa Beth" last="Duhaime">Melissa Beth Duhaime</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author><author><name sortKey="Peplies, Jorg" sort="Peplies, Jorg" uniqKey="Peplies J" first="Jörg" last="Peplies">Jörg Peplies</name><affiliation wicri:level="1"><nlm:aff id="I3">Ribocon GmbH D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Ribocon GmbH D-28359 Bremen</wicri:regionArea></affiliation></author><author><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><affiliation wicri:level="3"><nlm:aff id="I1">Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I2">Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Jacobs University Bremen gGmbH, D-28759 Bremen</wicri:regionArea><placeName><region type="land" nuts="3">Brême (Land)</region><settlement type="city">Brême</settlement></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Current sequencing technologies give access to sequence information for genomes and metagenomes at a tremendous speed. Subsequent data processing is mainly performed by automatic pipelines provided by the sequencing centers. Although, standardised workflows are desirable and useful in many respects, rational data mining, comparative genomics, and especially the interpretation of the sequence information in the biological context, demands for intuitive, flexible, and extendable solutions.</p></sec><sec><title>Results</title><p>The JCoast software tool was primarily designed to analyse and compare (meta)genome sequences of prokaryotes. Based on a pre-computed GenDB database project, JCoast offers a flexible graphical user interface (GUI), as well as an application programming interface (API) that facilitates back-end data access. JCoast offers individual, cross genome-, and metagenome analysis, and assists the biologist in exploration of large and complex datasets.</p></sec><sec><title>Conclusion</title><p>JCoast combines all functions required for the mining, annotation, and interpretation of (meta)genomic data. The lightweight software solution allows the user to easily take advantage of advanced back-end database structures by providing a programming and graphical user interface to answer biological questions. JCoast is available at the project homepage.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li></country><region><li>Brême (Land)</li></region><settlement><li>Brême</li></settlement></list><tree><country name="Allemagne"><region name="Brême (Land)"><name sortKey="Richter, Michael" sort="Richter, Michael" uniqKey="Richter M" first="Michael" last="Richter">Michael Richter</name></region><name sortKey="Duhaime, Melissa Beth" sort="Duhaime, Melissa Beth" uniqKey="Duhaime M" first="Melissa Beth" last="Duhaime">Melissa Beth Duhaime</name><name sortKey="Duhaime, Melissa Beth" sort="Duhaime, Melissa Beth" uniqKey="Duhaime M" first="Melissa Beth" last="Duhaime">Melissa Beth Duhaime</name><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><name sortKey="Glockner, Frank Oliver" sort="Glockner, Frank Oliver" uniqKey="Glockner F" first="Frank Oliver" last="Glöckner">Frank Oliver Glöckner</name><name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name><name sortKey="Kostadinov, Ivaylo" sort="Kostadinov, Ivaylo" uniqKey="Kostadinov I" first="Ivaylo" last="Kostadinov">Ivaylo Kostadinov</name><name sortKey="Kottmann, Renzo" sort="Kottmann, Renzo" uniqKey="Kottmann R" first="Renzo" last="Kottmann">Renzo Kottmann</name><name sortKey="Kottmann, Renzo" sort="Kottmann, Renzo" uniqKey="Kottmann R" first="Renzo" last="Kottmann">Renzo Kottmann</name><name sortKey="Lombardot, Thierry" sort="Lombardot, Thierry" uniqKey="Lombardot T" first="Thierry" last="Lombardot">Thierry Lombardot</name><name sortKey="Peplies, Jorg" sort="Peplies, Jorg" uniqKey="Peplies J" first="Jörg" last="Peplies">Jörg Peplies</name><name sortKey="Richter, Michael" sort="Richter, Michael" uniqKey="Richter M" first="Michael" last="Richter">Michael Richter</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 000D66 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000D66 | 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= PMC:2311307
|texte= JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:18380896" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a CyberinfraV1
| This area was generated with Dilib version V0.6.25. |  |