MetaBlasts: tracing protein tyrosine phosphatase gene family roots from Man to Drosophila melanogaster and Caenorhabditis elegans genomes.
At increasing speed, sequencing data are being made public from both complex and simple life forms. Although biomedical interests tend to focus on mammalian genes, only simple organisms allow rapid genetic manipulation and functional analysis. A prerequisite for the meaningful extrapolation of gene functional studies from invertebrates to man is that the orthologs under study are unambiguously linked. However, identifying orthologs is not trivial, especially where large gene families are involved. We present here an automated sequence analysis procedure that allows a rapid visualization of most likely ortholog pairs. We illustrate the utility of this approach for the human gene family of protein tyrosine phosphatases (PTPs) as compared with the full set of Caenorhabditis elegans and Drosophila melanogaster conceptual ORFs. The approach is based on a reciprocal series of BLAST searches, which are automatically stored and represented in an HTML-formatted table. We have used this 'MetaBlast' approach to compile lists of human PTPs and their worm and fly orthologs. Many of these PTP orthologs had not been previously identified as such.
Serono Pharmaceutical Research Institute, 14 chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland.
S
S
Wälchli
J
J
Colinge
R
R
Hooft van Huijsduijnen
D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000201:enzymology / Q000235:genetics; D016208:Databases, Factual; D004331:Drosophila melanogaster / Q000201:enzymology / Q000235:genetics; D006801:Humans; D016366:Open Reading Frames; D017027:Protein Tyrosine Phosphatases / Q000235:genetics*
D017027:Protein Tyrosine Phosphatases