Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Identifieur interne : 000362 ( Ncbi/Merge ); précédent : 000361; suivant : 000363Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
Auteurs : Thomas J. Sharpton [États-Unis] ; Guillaume Jospin [États-Unis] ; Dongying Wu [États-Unis] ; Morgan Gi Langille [Canada] ; Katherine S. Pollard [États-Unis] ; Jonathan A. Eisen [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Abstract
New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences.
We implemented fully automated and high-throughput procedures to
We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (
Url:
DOI: 10.1186/1471-2105-13-264
PubMed: 23061897
PubMed Central: 3481395
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences.</p>
</sec>
<sec><title>Results</title>
<p>We implemented fully automated and high-throughput procedures to <italic>de novo</italic>
cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses.</p>
</sec>
<sec><title>Conclusions</title>
<p>We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (<ext-link ext-link-type="uri" xlink:href="http://edhar.genomecenter.ucdavis.edu/sifting_families/">http://edhar.genomecenter.ucdavis.edu/sifting_families/</ext-link>
).</p>
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<contrib-group><contrib contrib-type="author" corresp="yes" equal-contrib="yes" id="A1"><name><surname>Sharpton</surname>
<given-names>Thomas J</given-names>
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<contrib contrib-type="author" equal-contrib="yes" id="A2"><name><surname>Jospin</surname>
<given-names>Guillaume</given-names>
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<given-names>Dongying</given-names>
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<xref ref-type="aff" rid="I7">7</xref>
<email>dongyingwu1@gmail.com</email>
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<given-names>Morgan GI</given-names>
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<contrib contrib-type="author" id="A5"><name><surname>Pollard</surname>
<given-names>Katherine S</given-names>
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<email>katherine.pollard@gladstone.ucsf.edu</email>
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<contrib contrib-type="author" id="A6"><name><surname>Eisen</surname>
<given-names>Jonathan A</given-names>
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<email>jaeisen@ucdavis.edu</email>
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The J. David Gladstone Institutes, University of California San Francisco, San Francisco, CA, 94158, USA</aff>
<aff id="I2"><label>2</label>
UC Davis Genome Center, University of California, Davis, Davis, CA, 95616, USA</aff>
<aff id="I3"><label>3</label>
Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada</aff>
<aff id="I4"><label>4</label>
Department of Epidemiology & Biostatistics, Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA</aff>
<aff id="I5"><label>5</label>
Deptartment of Evolution and Ecology, University of California, Davis, Davis, CA, 95616, USA</aff>
<aff id="I6"><label>6</label>
Deptartment of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, 95616, USA</aff>
<aff id="I7"><label>7</label>
Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA</aff>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>10</month>
<year>2012</year>
</pub-date>
<volume>13</volume>
<fpage>264</fpage>
<lpage>264</lpage>
<history><date date-type="received"><day>8</day>
<month>6</month>
<year>2012</year>
</date>
<date date-type="accepted"><day>9</day>
<month>10</month>
<year>2012</year>
</date>
</history>
<permissions><copyright-statement>Copyright ©2012 Sharpton et al.; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>Sharpton et al.; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-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">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.</license-p>
</license>
</permissions>
<self-uri xlink:href="http://www.biomedcentral.com/1471-2105/13/264"></self-uri>
<abstract><sec><title>Background</title>
<p>New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences.</p>
</sec>
<sec><title>Results</title>
<p>We implemented fully automated and high-throughput procedures to <italic>de novo</italic>
cluster proteins into families based upon global alignment similarity. Our approach employs an iterative clustering strategy in which homologs of known families are sifted out of the search for new families. The resulting reduction in computational complexity enables us to rapidly identify novel protein families found in new genomes and to perform efficient, automated updates that keep pace with genome sequencing. We refer to protein families identified through this approach as “Sifting Families,” or SFams. Our analysis of ~10.5 million protein sequences from 2,928 genomes identified 436,360 SFams, many of which are not represented in other protein family databases. We validated the quality of SFam clustering through statistical as well as network topology–based analyses.</p>
</sec>
<sec><title>Conclusions</title>
<p>We describe the rapid identification of SFams and demonstrate how they can be used to annotate genomes and metagenomes. The SFam database catalogs protein-family quality metrics, multiple sequence alignments, hidden Markov models, and phylogenetic trees. Our source code and database are publicly available and will be subject to frequent updates (<ext-link ext-link-type="uri" xlink:href="http://edhar.genomecenter.ucdavis.edu/sifting_families/">http://edhar.genomecenter.ucdavis.edu/sifting_families/</ext-link>
).</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>Canada</li>
<li>États-Unis</li>
</country>
</list>
<tree><country name="États-Unis"><noRegion><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J" last="Sharpton">Thomas J. Sharpton</name>
</noRegion>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Eisen, Jonathan A" sort="Eisen, Jonathan A" uniqKey="Eisen J" first="Jonathan A" last="Eisen">Jonathan A. Eisen</name>
<name sortKey="Jospin, Guillaume" sort="Jospin, Guillaume" uniqKey="Jospin G" first="Guillaume" last="Jospin">Guillaume Jospin</name>
<name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name>
<name sortKey="Pollard, Katherine S" sort="Pollard, Katherine S" uniqKey="Pollard K" first="Katherine S" last="Pollard">Katherine S. Pollard</name>
<name sortKey="Wu, Dongying" sort="Wu, Dongying" uniqKey="Wu D" first="Dongying" last="Wu">Dongying Wu</name>
<name sortKey="Wu, Dongying" sort="Wu, Dongying" uniqKey="Wu D" first="Dongying" last="Wu">Dongying Wu</name>
</country>
<country name="Canada"><noRegion><name sortKey="Langille, Morgan Gi" sort="Langille, Morgan Gi" uniqKey="Langille M" first="Morgan Gi" last="Langille">Morgan Gi Langille</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>
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