Abstract
In this paper, we apply two different parallel programming model, the message passing model using Message Passing Interface (MPI) and the multithreaded model using Pthreads, to protein sequence homologous search. The protein sequence homologous search uses Hirschberg algorithm for the pair-wise sequence alignment. The performance of the homologous search using the MPI-Pthread is compared to the implementation using pure message passing programming model MPI. The evaluation results show that there is a 50% decrease in computing time when the parallel homologous search is implemented using MPI-Phtreads compared to when using MPI.