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Bioinformatics Advance Access originally published online on June 5, 2008
Bioinformatics 2008 24(14):1568-1574; doi:10.1093/bioinformatics/btn257
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Hyperbolic SOM-based clustering of DNA fragment features for taxonomic visualization and classification

Christian Martin 1,2,*, Naryttza N. Diaz 1,2, Jörg Ontrup 1 and Tim W. Nattkemper 1

1AG Applied Neuroinformatics, Technical Faculty, Bielefeld University and 2Graduate School Bioinformatics and Genome Research, CeBiTec, Bielefeld University, Bielefeld, Germany

*To whom correspondence should be addressed.


  Abstract

Motivation: Modern high-throughput sequencing technologies enable the simultaneous analysis of organisms in an environment. The analysis of species diversity and the binning of DNA fragments of non-sequenced species for assembly are two major challenges in sequence analysis. To achieve reasonable binnings and classifications, DNA fragment structure has to be represented appropriately, so it can be processed by machine learning algorithms.

Results: Hierarchically growing hyperbolic Self-Organizing maps (H 2SOMs) are trained to cluster small variable-length DNA fragments (0.2–50 kb) of 350 prokaryotic organisms at six taxonomic ranks Superkingdom, Phylum, Class, Order, Genus and Species in the Tree of Life. DNA fragments are mapped to three different types of feature vectors based on the genomic signature: basic features, features considering the importance of oligonucleotide patterns as well as contrast enhanced features. The H 2SOM classifier achieves high classification rates while at the same time its visualization allows further insights into the projected data and has the potential to support binning of short sequence reads, because DNA fragments can be grouped into phylogenetic groups.

Availability: An implementation of the H 2HSOM classifier in Matlab is provided at www.techfak.uni-bielefeld.de/ags/ani/projects/HHSOMSeqData

Contact: christian.martin{at}uni-bielefeld.de

Supplementary Information: Supplementary data are available at Bioinformatics online.

Associate Editor: Limsoon Wong

Received on February 22, 2008; revised on May 16, 2008; accepted on June 3, 2008

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