Identifying distantly related protein sequences

The most powerful method available today for inferring the biological function of a gene (or the protein that it encodes) from its sequence is similarity searching on protein and DNA sequence databases. With the development of rapid methods for sequence comparison, both with heuristic algorithms and powerful parallel computers, discoveries based solely on sequence homology have become routine. Indeed, the vast majority of the gene identifications in the recent descriptions of the Haemophilus influenzae (Fleischmann et ai, 1995), Mycoplasma genitalium (Fraser et ai, 1995), yeast (Dujon, 1996) and Methanococcus janesscii (Bult et ai, 1996) genomes are based only on protein sequence similarity. As more complete genomes become available, protein sequence comparison will become an even more powerful tool for understanding biological function.