Dataset Information

PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.

ABSTRACT:

Background

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.

Results

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.

Conclusions

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 http://www.biochem.uni-luebeck.de/public/software/phylomap.html.

SUBMITTER: Zhang J

PROVIDER: S-EPMC3142226 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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Publications

PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.

Zhang Jiajie J Mamlouk Amir Madany AM Martinetz Thomas T Chang Suhua S Wang Jing J Hilgenfeld Rolf R

BMC bioinformatics 20110620

<h4>Background</h4>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 t ...[more]

PMID: 21689434

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Dataset Information

PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.

Background

Results

Conclusions

Publications

PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome.

Similar Datasets

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