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Fast and efficient protein sequence alignment and comparison algorithms have become significance as the size of databases grow very rapidly. This paper introduces a parallel algorithm for Hashing-N-Gram-Hirschberg (HNGH) algorithm. The HNGH algorithm is an extension of N-Gram-Hirschberg (NGH) algorithm which was proposed by Abdul Rashid in 2007. The parallel algorithm is proposed to speed up the sequential HNGH when run on large database. Our parallel algorithm has two levels of parallelization, one on processors level and the other one on the cores level. By testing our previous work with different Gram lengths ranges from 3-6 letters, HNGH algorithm outperforms the former algorithm (NGH algorithm) in most cases. The parallel algorithm shows an enhancement in the execution time but the speed up is a bit low because of the high communication among processers and the high dependency among the tasks.