Direct Comarison DNA and Amino Acid Sequences Based on a Dynamic Programming Method

Abstract

We have developed a method based on a dynamic programming method, that enables us 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 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.