NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Identifieur interne : 000175 ( Ncbi/Merge ); précédent : 000174; suivant : 000176NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads
Auteurs : Gail L. Rosen ; Erin R. Reichenberger ; Aaron M. Rosenfeld [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2010.
Abstract
Url:
DOI: 10.1093/bioinformatics/btq619
PubMed: 21062764
PubMed Central: 3008645
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads</title><author><name sortKey="Rosen, Gail L" sort="Rosen, Gail L" uniqKey="Rosen G" first="Gail L." last="Rosen">Gail L. Rosen</name><affiliation><nlm:aff id="AFF1">Department of Electrical and Computer Engineering,</nlm:aff></affiliation></author><author><name sortKey="Reichenberger, Erin R" sort="Reichenberger, Erin R" uniqKey="Reichenberger E" first="Erin R." last="Reichenberger">Erin R. Reichenberger</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">School of Biomedical Engineering, Science, and Health Systems</nlm:aff><wicri:noCountry code="subfield">and Health Systems</wicri:noCountry></affiliation></author><author><name sortKey="Rosenfeld, Aaron M" sort="Rosenfeld, Aaron M" uniqKey="Rosenfeld A" first="Aaron M." last="Rosenfeld">Aaron M. Rosenfeld</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Department of Computer Science, Drexel University, Philadelphia, PA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Drexel University, Philadelphia, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21062764</idno><idno type="pmc">3008645</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008645</idno><idno type="RBID">PMC:3008645</idno><idno type="doi">10.1093/bioinformatics/btq619</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000501</idno><idno type="wicri:Area/Pmc/Curation">000501</idno><idno type="wicri:Area/Pmc/Checkpoint">000566</idno><idno type="wicri:Area/Ncbi/Merge">000175</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads</title><author><name sortKey="Rosen, Gail L" sort="Rosen, Gail L" uniqKey="Rosen G" first="Gail L." last="Rosen">Gail L. Rosen</name><affiliation><nlm:aff id="AFF1">Department of Electrical and Computer Engineering,</nlm:aff></affiliation></author><author><name sortKey="Reichenberger, Erin R" sort="Reichenberger, Erin R" uniqKey="Reichenberger E" first="Erin R." last="Reichenberger">Erin R. Reichenberger</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">School of Biomedical Engineering, Science, and Health Systems</nlm:aff><wicri:noCountry code="subfield">and Health Systems</wicri:noCountry></affiliation></author><author><name sortKey="Rosenfeld, Aaron M" sort="Rosenfeld, Aaron M" uniqKey="Rosenfeld A" first="Aaron M." last="Rosenfeld">Aaron M. Rosenfeld</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Department of Computer Science, Drexel University, Philadelphia, PA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Drexel University, Philadelphia, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1367-4811</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold> Datasets from high-throughput sequencing technologies have yielded a vast amount of data about organisms in environmental samples. Yet, it is still a challenge to assess the exact organism content in these samples because the task of taxonomic classification is too computationally complex to annotate all reads in a dataset. An easy-to-use webserver is needed to process these reads. While many methods exist, only a few are publicly available on webservers, and out of those, most do not annotate all reads.</p><p><bold>Results:</bold> We introduce a webserver that implements the naïve Bayes classifier (NBC) to classify all metagenomic reads to their best taxonomic match. Results indicate that NBC can assign next-generation sequencing reads to their taxonomic classification and can find significant populations of genera that other classifiers may miss.</p><p><bold>Availability:</bold> Publicly available at: <ext-link ext-link-type="uri" xlink:href="http://nbc.ece.drexel.edu">http://nbc.ece.drexel.edu</ext-link>.</p><p><bold>Contact:</bold> <email>gailr@ece.drexel.edu</email></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Altschul, Sf" uniqKey="Altschul S">SF Altschul</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gerlach, W" uniqKey="Gerlach W">W Gerlach</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hery, M" uniqKey="Hery M">M Hery</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huson, De" uniqKey="Huson D">DE Huson</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mchardy, Ac" uniqKey="Mchardy A">AC McHardy</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Meyer, F" uniqKey="Meyer F">F Meyer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nolan, M" uniqKey="Nolan M">M Nolan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Overbeek, R" uniqKey="Overbeek R">R Overbeek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pond, Sk" uniqKey="Pond S">SK Pond</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rosen, Gl" uniqKey="Rosen G">GL Rosen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rosen, Gl" uniqKey="Rosen G">GL Rosen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schluter, A" uniqKey="Schluter A">A Schlüter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Seshadri, R" uniqKey="Seshadri R">R Seshadri</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vinneras, B" uniqKey="Vinneras B">B Vinneras</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">bioinformatics</journal-id><journal-id journal-id-type="hwp">bioinfo</journal-id><journal-title-group><journal-title>Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1367-4803</issn><issn pub-type="epub">1367-4811</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21062764</article-id><article-id pub-id-type="pmc">3008645</article-id><article-id pub-id-type="doi">10.1093/bioinformatics/btq619</article-id><article-id pub-id-type="publisher-id">btq619</article-id><article-categories><subj-group subj-group-type="heading"><subject>Applications Note</subject><subj-group><subject>Genome Analysis</subject></subj-group></subj-group></article-categories><title-group><article-title>NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Rosen</surname><given-names>Gail L.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Reichenberger</surname><given-names>Erin R.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Rosenfeld</surname><given-names>Aaron M.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Electrical and Computer Engineering,<sup>2</sup>School of Biomedical Engineering, Science, and Health Systems and<sup>3</sup>Department of Computer Science, Drexel University, Philadelphia, PA, USA</aff><author-notes><corresp id="COR1">* To whom correspondence should be addressed.</corresp><fn><p>Associate Editor: John Quackenbush</p></fn></author-notes><pub-date pub-type="ppub"><day>1</day><month>1</month><year>2011</year></pub-date><pub-date pub-type="epub"><day>8</day><month>11</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>8</day><month>11</month><year>2010</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>27</volume><issue>1</issue><fpage>127</fpage><lpage>129</lpage><history><date date-type="received"><day>2</day><month>8</month><year>2010</year></date><date date-type="rev-recd"><day>12</day><month>10</month><year>2010</year></date><date date-type="accepted"><day>29</day><month>10</month><year>2010</year></date></history><permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press.</copyright-statement><copyright-year>2010</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p><bold>Motivation:</bold> Datasets from high-throughput sequencing technologies have yielded a vast amount of data about organisms in environmental samples. Yet, it is still a challenge to assess the exact organism content in these samples because the task of taxonomic classification is too computationally complex to annotate all reads in a dataset. An easy-to-use webserver is needed to process these reads. While many methods exist, only a few are publicly available on webservers, and out of those, most do not annotate all reads.</p><p><bold>Results:</bold> We introduce a webserver that implements the naïve Bayes classifier (NBC) to classify all metagenomic reads to their best taxonomic match. Results indicate that NBC can assign next-generation sequencing reads to their taxonomic classification and can find significant populations of genera that other classifiers may miss.</p><p><bold>Availability:</bold> Publicly available at: <ext-link ext-link-type="uri" xlink:href="http://nbc.ece.drexel.edu">http://nbc.ece.drexel.edu</ext-link>.</p><p><bold>Contact:</bold> <email>gailr@ece.drexel.edu</email></p></abstract></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region></list><tree><noCountry><name sortKey="Reichenberger, Erin R" sort="Reichenberger, Erin R" uniqKey="Reichenberger E" first="Erin R." last="Reichenberger">Erin R. Reichenberger</name><name sortKey="Rosen, Gail L" sort="Rosen, Gail L" uniqKey="Rosen G" first="Gail L." last="Rosen">Gail L. Rosen</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Rosenfeld, Aaron M" sort="Rosenfeld, Aaron M" uniqKey="Rosenfeld A" first="Aaron M." last="Rosenfeld">Aaron M. Rosenfeld</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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