New software called PROCRUSTES, described in the August 20 issue of the Proceedings of the National Academy of Sciences, can identify with remarkable accuracy human versions of genes found in other life forms. The product of a collaboration between an American and two Russian researchers, PROCRUSTES is considered far more useful than existing techniques if a related pattern is known.

"With this method, anything alive can serve as a template to find human genes. Mouse, chicken, frog the species doesn't matter," said coauthor Pavel Pevzner (University of Southern California).

Pevzner and his Russian collaborators, Mikhail S. Gelfand (Russian Academy of Science) and Andrey Mironov (Russian National Center for Biotechnology), devised a spliced-alignment algorithm and software tool that overcomes formidable obstacles. Human genes, which average about 2000 bp, are broken up into smaller segments called exons. The exons can be separated by millions of bases of noncoding DNA that sometimes mimic the exons.

As Pevzner explains, searching for exons is like trying to follow a magazine article that appears on pages 1, 16, 21, 74, and 87, with almost identical advertisements and other articles appearing between. PROCRUSTES helps by constructing a list of all the "pages" that are part of the "story," then automatically combining them into the set that makes the best fit.

The technique works best when a "target protein" from the nonhuman sample is available to guide the search. With such guidance, the method's accuracy often approaches 100%, the authors report. The new tool should prove particularly useful for researchers trying to pinpoint elusive human versions of cancer-causing genes already sequenced in mice and other species.

Articles on PROCRUSTES have appeared in Business Week, Investor's Business Daily, and BioWorld Today. The research was supported by grants from DOE, the Russian Fund for Fundamental Research, the Russian Human Genome Program, and the National Science Foundation's Young Investigator Program.