JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
Identifieur interne : 000044 ( Ncbi/Merge ); précédent : 000043; suivant : 000045JCoast – 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
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PMC:2311307Le document en format XML
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<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>
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<journal-title>BMC Bioinformatics</journal-title>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
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<article-id pub-id-type="doi">10.1186/1471-2105-9-177</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Software</subject>
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<title-group><article-title>JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes</article-title>
</title-group>
<contrib-group><contrib id="A1" contrib-type="author"><name><surname>Richter</surname>
<given-names>Michael</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>mrichter@mpi-bremen.de</email>
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<contrib id="A2" contrib-type="author"><name><surname>Lombardot</surname>
<given-names>Thierry</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>tlombard@mpi-bremen.de</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Kostadinov</surname>
<given-names>Ivaylo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>ikostadi@mpi-bremen.de</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Kottmann</surname>
<given-names>Renzo</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>rkottman@mpi-bremen.de</email>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Duhaime</surname>
<given-names>Melissa Beth</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>mduhaime@mpi-bremen.de</email>
</contrib>
<contrib id="A6" contrib-type="author"><name><surname>Peplies</surname>
<given-names>Jörg</given-names>
</name>
<xref ref-type="aff" rid="I3">3</xref>
<email>jpeplies@ribocon.com</email>
</contrib>
<contrib id="A7" corresp="yes" contrib-type="author"><name><surname>Glöckner</surname>
<given-names>Frank Oliver</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>fog@mpi-bremen.de</email>
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<aff id="I1"><label>1</label>
Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany</aff>
<aff id="I2"><label>2</label>
Jacobs University Bremen gGmbH, D-28759 Bremen, Germany</aff>
<aff id="I3"><label>3</label>
Ribocon GmbH D-28359 Bremen, Germany</aff>
<pub-date pub-type="collection"><year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>1</day>
<month>4</month>
<year>2008</year>
</pub-date>
<volume>9</volume>
<fpage>177</fpage>
<lpage>177</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2105/9/177"></ext-link>
<history><date date-type="received"><day>10</day>
<month>1</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>1</day>
<month>4</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008 Richter et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Richter et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Richter
Michael
mrichter@mpi-bremen.de
JCoast – A biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes
2008 BMC Bioinformatics 9(1): 177-. (2008) 1471-2105(2008)9:1<177> urn:ISSN:1471-2105 </pmc-comment>
</license>
</permissions>
<abstract><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>
</abstract>
</article-meta>
</front>
</pmc>
<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>
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