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

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 prealignment 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...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Gary W. Stuart, Michael W. Berry
• Keywords: BMCBI 2004, Eukaryotic Genomes, Genomes, Putative Orthologs