PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
Identifieur interne : 000C22 ( Main/Exploration ); précédent : 000C21; suivant : 000C23PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
Auteurs : Jiajie Zhang [Allemagne] ; Amir Madany Mamlouk [Allemagne] ; Thomas Martinetz [Allemagne] ; Suhua Chang [République populaire de Chine] ; Jing Wang [République populaire de Chine] ; Rolf Hilgenfeld [Allemagne, République populaire de Chine]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2011.
Abstract
Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome.
Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed.
The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at
Url:
DOI: 10.1186/1471-2105-12-248
PubMed: 21689434
PubMed Central: 3142226
Affiliations:
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Le document en format XML
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome.</p>
</sec>
<sec><title>Results</title>
<p>Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed.</p>
</sec>
<sec><title>Conclusions</title>
<p>The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.biochem.uni-luebeck.de/public/software/phylomap.html">http://www.biochem.uni-luebeck.de/public/software/phylomap.html</ext-link>
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</author>
<author><name sortKey="Huelsenbeck, Jp" uniqKey="Huelsenbeck J">JP Huelsenbeck</name>
</author>
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<author><name sortKey="Nielsen, R" uniqKey="Nielsen R">R Nielsen</name>
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</author>
<author><name sortKey="Harris, Dj" uniqKey="Harris D">DJ Harris</name>
</author>
<author><name sortKey="Scotland, Rw" uniqKey="Scotland R">RW Scotland</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hedtke, Sm" uniqKey="Hedtke S">SM Hedtke</name>
</author>
<author><name sortKey="Townsend, Tm" uniqKey="Townsend T">TM Townsend</name>
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<author><name sortKey="Hillis, Dm" uniqKey="Hillis D">DM Hillis</name>
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<author><name sortKey="Suzuki, A" uniqKey="Suzuki A">A Suzuki</name>
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<author><name sortKey="Oshitani, H" uniqKey="Oshitani H">H Oshitani</name>
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<author><name sortKey="Webby, Rj" uniqKey="Webby R">RJ Webby</name>
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<author><name sortKey="Bruno, Wj" uniqKey="Bruno W">WJ Bruno</name>
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<author><name sortKey="Bruns, L" uniqKey="Bruns L">L Bruns</name>
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<author><name sortKey="Meixenberger, K" uniqKey="Meixenberger K">K Meixenberger</name>
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<biblStruct><analytic><author><name sortKey="Stover, Bc" uniqKey="Stover B">BC Stover</name>
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</TEI>
<affiliations><list><country><li>Allemagne</li>
<li>République populaire de Chine</li>
</country>
<region><li>Hambourg</li>
</region>
<settlement><li>Hambourg</li>
<li>Pékin</li>
</settlement>
</list>
<tree><country name="Allemagne"><noRegion><name sortKey="Zhang, Jiajie" sort="Zhang, Jiajie" uniqKey="Zhang J" first="Jiajie" last="Zhang">Jiajie Zhang</name>
</noRegion>
<name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name>
<name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name>
<name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name>
<name sortKey="Mamlouk, Amir Madany" sort="Mamlouk, Amir Madany" uniqKey="Mamlouk A" first="Amir Madany" last="Mamlouk">Amir Madany Mamlouk</name>
<name sortKey="Mamlouk, Amir Madany" sort="Mamlouk, Amir Madany" uniqKey="Mamlouk A" first="Amir Madany" last="Mamlouk">Amir Madany Mamlouk</name>
<name sortKey="Martinetz, Thomas" sort="Martinetz, Thomas" uniqKey="Martinetz T" first="Thomas" last="Martinetz">Thomas Martinetz</name>
<name sortKey="Martinetz, Thomas" sort="Martinetz, Thomas" uniqKey="Martinetz T" first="Thomas" last="Martinetz">Thomas Martinetz</name>
<name sortKey="Zhang, Jiajie" sort="Zhang, Jiajie" uniqKey="Zhang J" first="Jiajie" last="Zhang">Jiajie Zhang</name>
<name sortKey="Zhang, Jiajie" sort="Zhang, Jiajie" uniqKey="Zhang J" first="Jiajie" last="Zhang">Jiajie Zhang</name>
</country>
<country name="République populaire de Chine"><noRegion><name sortKey="Chang, Suhua" sort="Chang, Suhua" uniqKey="Chang S" first="Suhua" last="Chang">Suhua Chang</name>
</noRegion>
<name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name>
<name sortKey="Wang, Jing" sort="Wang, Jing" uniqKey="Wang J" first="Jing" last="Wang">Jing Wang</name>
</country>
</tree>
</affiliations>
</record>
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