Direct Comparison DNA and Amino Acid Sequences Based on a Dynamic Program ming Method

Naoko Kasahara (kasahara@crl.hitachi.co.jp)
Susumu Hiraoka (hiraoka@crl.hitachi.co.jp)
Keiichi Nagai (k-nagai@crl.hitachi.co.jp)

Central Research Laboratory, Hitachi, Ltd.,
1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185, Japan

We have developed a method based on a dynamic programming method, that enables us to directly compare DNA and amino acid sequences. This method makes it possible to find homologies between translated DNA sequences and amino acid sequences by recognizing gaps in both types of sequences. This method allows higher sensitivity and specificity than is possible with BLASTX, which has a similar function. To reduce the computation time, we performed a parallel computation on a workstation cluster using a PVM ( Parallel Virtual Machine ) programming.