Fast Comparison of a DNA Sequence with a Protein Sequence Database

We describe a computer program, named DNA-Protein Search (DPS), for comparing a megabase DNA sequence with a protein sequence database. The DPS program addresses the problems of frameshifts and introns in the DNA sequence. The DPS program was used to compare each of the following sequences with the Swiss-Prot database: the 1.8-megabase sequence of the Haemophilus influenzae Rd genome, the 0.58-megabase sequence of the Mycoplasma genitalium genome, and the 0.56-megabase sequence of Saccharomyces cerevisiae chromosome VIII. The comparisons found new regions that are similar to protein sequences. The sensitivity of DPS was evaluated using as test data the known coding regions of the three DNA sequences. The results demonstrate that the DPS program is a useful tool for finding the coding regions of the DNA sequence. The DPS program uses an order of magnitude less computer memory and is several times faster than the BLASTX program.