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 comple x and simple life forms. Although biomedical interests tend to focus on mam malian genes, only simple organisms allow rapid genetic manipulation and fu nctional analysis. A prerequisite for the meaningful extrapolation of gene functional studies from invertebrates to man is that the orthologs under st udy are unambiguously linked. However, identifying orthologs is not trivial , especially where large gene families are involved. We present here an aut omated sequence analysis procedure that allows a rapid visualization of mos t 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 concept ual ORFs. The approach is based on a reciprocal series of BLAST searches, w hich are automatically stored and represented in an HTML-formatted table. W e have used this 'MetaBlast' approach to compile lists of human PTPs and th eir worm and fly orthologs. Many of these PTP orthologs had not been previo usly identified as such. (C) 2000 Elsevier Science B.V. All rights reserved .