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Bioinformatics Advance Access published online on April 13, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl146
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 6, 2006
Revised April 11, 2006
Accepted April 11, 2006

Article

Ribosomal RNA as molecular barcodes: a simple correlation analysis without sequence alignment

K. H. Chu 1 *, C. P. Li 1, and J. Qi 2

1 Department of Biology, The Chinese University of Hong Kong, Hong Kong, China
2 Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802, USA

* To whom correspondence should be addressed.
K. H. Chu, E-mail: kahouchu{at}cuhk.edu.hk


  Abstract

Motivation: We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors derived from nucleotide strings. We tested this method with seven rRNA (including 12S, 16S, 18S, 26S and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species.

Result: Our results indicate that grouping of taxa based on composition vector analysis is always in good agreement with the phylogenetic trees generated by traditional approaches, although in some cases the relationships among the higher systemic groups may differ. The effectiveness of our analysis might be related to the length and divergence among sequences in a dataset. Nevertheless, the correct grouping of sequences and accurate assignment of unknown taxa make our analysis a reliable and convenient approach in analyzing unaligned sequence datasets of various rRNAs for barcoding purposes.

Availability: The newly designed software (CVTree 1.0) is publicly available at the Composition Vector Tree (CVTree) web server http://cvtree.cbi.pku.edu.cn.

Associate Editor: Chris Stoeckert
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