PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
Identifieur interne : 000903 ( Pmc/Curation ); précédent : 000902; suivant : 000904PhyloMap: 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
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DOI: 10.1186/1471-2105-12-248
PubMed: 21689434
PubMed Central: 3142226
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genome</title><author><name sortKey="Zhang, Jiajie" sort="Zhang, Jiajie" uniqKey="Zhang J" first="Jiajie" last="Zhang">Jiajie Zhang</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff 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160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute for Neuro- and Bioinformatics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation></author><author><name sortKey="Martinetz, Thomas" sort="Martinetz, Thomas" uniqKey="Martinetz T" first="Thomas" last="Martinetz">Thomas Martinetz</name><affiliation wicri:level="1"><nlm:aff id="I2">Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Institute for Neuro- and Bioinformatics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country 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xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101</wicri:regionArea></affiliation></author><author><name sortKey="Hilgenfeld, Rolf" sort="Hilgenfeld, Rolf" uniqKey="Hilgenfeld R" first="Rolf" last="Hilgenfeld">Rolf Hilgenfeld</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I5">Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I6">Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Rd., Shanghai 201203, China</nlm:aff><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Rd., Shanghai 201203</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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></p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Procter, Jb" uniqKey="Procter J">JB Procter</name></author><author><name sortKey="Thompson, J" uniqKey="Thompson J">J Thompson</name></author><author><name sortKey="Letunic, I" uniqKey="Letunic I">I Letunic</name></author><author><name sortKey="Creevey, C" uniqKey="Creevey C">C Creevey</name></author><author><name sortKey="Jossinet, F" uniqKey="Jossinet F">F Jossinet</name></author><author><name sortKey="Barton, Gj" uniqKey="Barton G">GJ Barton</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pavlopoulos, Ga" uniqKey="Pavlopoulos G">GA Pavlopoulos</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Bioinformatics</journal-id><journal-title-group><journal-title>BMC Bioinformatics</journal-title></journal-title-group><issn pub-type="epub">1471-2105</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21689434</article-id><article-id pub-id-type="pmc">3142226</article-id><article-id pub-id-type="publisher-id">1471-2105-12-248</article-id><article-id pub-id-type="doi">10.1186/1471-2105-12-248</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Zhang</surname><given-names>Jiajie</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>zhangjiajie@biochem.uni-luebeck.de</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Mamlouk</surname><given-names>Amir Madany</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>madany@inb.uni-luebeck.de</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Martinetz</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I3">3</xref><email>martinetz@inb.uni-luebeck.de</email></contrib><contrib contrib-type="author" id="A4"><name><surname>Chang</surname><given-names>Suhua</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>changsh@psych.ac.cn</email></contrib><contrib contrib-type="author" id="A5"><name><surname>Wang</surname><given-names>Jing</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>wangjing@psych.ac.cn</email></contrib><contrib contrib-type="author" corresp="yes" id="A6"><name><surname>Hilgenfeld</surname><given-names>Rolf</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><xref ref-type="aff" rid="I5">5</xref><xref ref-type="aff" rid="I6">6</xref><email>hilgenfeld@biochem.uni-luebeck.de</email></contrib></contrib-group><aff id="I1"><label>1</label>Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</aff><aff id="I2"><label>2</label>Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</aff><aff id="I3"><label>3</label>Institute for Neuro- and Bioinformatics, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany</aff><aff id="I4"><label>4</label>Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China</aff><aff id="I5"><label>5</label>Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Building 22a, Notkestr. 85, 22603 Hamburg, Germany</aff><aff id="I6"><label>6</label>Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Rd., Shanghai 201203, China</aff><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>20</day><month>6</month><year>2011</year></pub-date><volume>12</volume><fpage>248</fpage><lpage>248</lpage><history><date date-type="received"><day>19</day><month>1</month><year>2011</year></date><date date-type="accepted"><day>20</day><month>6</month><year>2011</year></date></history><permissions><copyright-statement>Copyright ©2011 Zhang et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>Zhang 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/1471-2105/12/248"></self-uri><abstract><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></p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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|area= H2N2V1
|flux= Pmc
|étape= Curation
|type= RBID
|clé= PMC:3142226
|texte= PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:21689434" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a H2N2V1
| This area was generated with Dilib version V0.6.33. |  |