A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Identifieur interne : 000683 ( Pmc/Checkpoint ); précédent : 000682; suivant : 000684A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Auteurs : Sheila Podell [États-Unis] ; Terry Gaasterland [États-Unis] ; Eric E. Allen [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2008.
Abstract
The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands.
The
The
Url:
DOI: 10.1186/1471-2105-9-419
PubMed: 18840280
PubMed Central: 2573894
Affiliations:
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. <italic>DarkHorse</italic>
, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not.</p>
</sec>
<sec><title>Description</title>
<p>The <italic>DarkHorse </italic>
algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searchable relational database, called the <italic>DarkHorse </italic>
HGT Candidate Resource <ext-link ext-link-type="uri" xlink:href="http://darkhorse.ucsd.edu"></ext-link>
. Users can select individual genomes or groups of genomes to screen by LPI score, search for protein functions by descriptive annotation or amino acid sequence similarity, or select proteins with unusual G+C composition in their underlying coding sequences. The search engine reports LPI scores for match partners as well as query sequences, providing the opportunity to explore whether potential HGT donor sequences are phylogenetically typical or atypical within their own genomes. This information can be used to predict whether or not sufficient information is available to build a well-supported phylogenetic tree using the potential donor sequence.</p>
</sec>
<sec><title>Conclusion</title>
<p>The <italic>DarkHorse </italic>
HGT Candidate database provides a powerful, flexible set of tools for identifying phylogenetically atypical proteins, allowing researchers to explore both individual HGT events in single genomes, and large-scale HGT patterns among protein families and genome groups. Although the <italic>DarkHorse </italic>
algorithm cannot, by itself, provide definitive proof of horizontal gene transfer, it is a flexible, powerful tool that can be combined with slower, more rigorous methods in situations where these other methods could not otherwise be applied.</p>
</sec>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id>
<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-meta><article-id pub-id-type="pmid">18840280</article-id>
<article-id pub-id-type="pmc">2573894</article-id>
<article-id pub-id-type="publisher-id">1471-2105-9-419</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-9-419</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Database</subject>
</subj-group>
</article-categories>
<title-group><article-title>A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the <italic>DarkHorse </italic>
algorithm</article-title>
</title-group>
<contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Podell</surname>
<given-names>Sheila</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>spodell@ucsd.edu</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Gaasterland</surname>
<given-names>Terry</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>tgaasterland@ucsd.edu</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Allen</surname>
<given-names>Eric E</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<xref ref-type="aff" rid="I2">2</xref>
<email>eallen@ucsd.edu</email>
</contrib>
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<aff id="I1"><label>1</label>
Marine Biology Research Division, Scripps Institution of Oceanography University of California at San Diego, La Jolla, CA 92093 USA</aff>
<aff id="I2"><label>2</label>
Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093 USA</aff>
<pub-date pub-type="collection"><year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>7</day>
<month>10</month>
<year>2008</year>
</pub-date>
<volume>9</volume>
<fpage>419</fpage>
<lpage>419</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2105/9/419"></ext-link>
<history><date date-type="received"><day>14</day>
<month>5</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>7</day>
<month>10</month>
<year>2008</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2008 Podell et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Podell 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>
Podell
Sheila
spodell@ucsd.edu
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
2008 BMC Bioinformatics 9(1): 419-. (2008) 1471-2105(2008)9:1<419> urn:ISSN:1471-2105 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection of high-quality, automated HGT prediction data based on phylogenetic evidence has previously been impractical for large numbers of genomes at once, due to prohibitive computational demands. <italic>DarkHorse</italic>
, a recently described statistical method for discovering phylogenetically atypical genes on a genome-wide basis, provides a means to solve this problem through lineage probability index (LPI) ranking scores. LPI scores inversely reflect phylogenetic distance between a test amino acid sequence and its closest available database matches. Proteins with low LPI scores are good horizontal gene transfer candidates; those with high scores are not.</p>
</sec>
<sec><title>Description</title>
<p>The <italic>DarkHorse </italic>
algorithm has been applied to 955 microbial genome sequences, and the results organized into a web-searchable relational database, called the <italic>DarkHorse </italic>
HGT Candidate Resource <ext-link ext-link-type="uri" xlink:href="http://darkhorse.ucsd.edu"></ext-link>
. Users can select individual genomes or groups of genomes to screen by LPI score, search for protein functions by descriptive annotation or amino acid sequence similarity, or select proteins with unusual G+C composition in their underlying coding sequences. The search engine reports LPI scores for match partners as well as query sequences, providing the opportunity to explore whether potential HGT donor sequences are phylogenetically typical or atypical within their own genomes. This information can be used to predict whether or not sufficient information is available to build a well-supported phylogenetic tree using the potential donor sequence.</p>
</sec>
<sec><title>Conclusion</title>
<p>The <italic>DarkHorse </italic>
HGT Candidate database provides a powerful, flexible set of tools for identifying phylogenetically atypical proteins, allowing researchers to explore both individual HGT events in single genomes, and large-scale HGT patterns among protein families and genome groups. Although the <italic>DarkHorse </italic>
algorithm cannot, by itself, provide definitive proof of horizontal gene transfer, it is a flexible, powerful tool that can be combined with slower, more rigorous methods in situations where these other methods could not otherwise be applied.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
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<region><li>Californie</li>
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<name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E" last="Allen">Eric E. Allen</name>
<name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E" last="Allen">Eric E. Allen</name>
<name sortKey="Gaasterland, Terry" sort="Gaasterland, Terry" uniqKey="Gaasterland T" first="Terry" last="Gaasterland">Terry Gaasterland</name>
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