Research article

An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage

Gary W Stuart^1,2 and Michael W Berry³

¹Department of Life Sciences, Indiana State University, Terre Haute, IN 47809, USA

²Visiting Scientist, Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA

³Department of Computer Science, University of Tennessee, Knoxville TN 37996-3450, USA

author email corresponding author email

BMC Bioinformatics 2004, 5:204doi:10.1186/1471-2105-5-204

Published:	17 December 2004

Abstract

Background

Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putative orthologs in order to reduce the effective size of the dataset and provide a reasonably high but unknown fraction of correctly aligned homologous sites for comparison. As an alternative, highly efficient methods that do not require the pre-alignment of operationally defined orthologs are also being explored.

Results

A non-alignment method based on the Singular Value Decomposition (SVD) was used to compare the predicted protein complement of nine whole eukaryotic genomes ranging from yeast to man. This analysis resulted in the simultaneous identification and definition of a large number of well conserved motifs and gene families, and produced a species tree supporting one of two conflicting hypotheses of metazoan relationships.

Conclusions

Our SVD-based analysis of the entire protein complement of nine whole eukaryotic genomes suggests that highly conserved motifs and gene families can be identified and effectively compared in a single coherent definition space for the easy extraction of gene and species trees. While this occurs without the explicit definition of orthologs or homologous sites, the analysis can provide a basis for these definitions.