Comparison Algorithm of Protein Sequences by Introducing a Lookup Table

Shin-ichi NAKAYAMA* and Masayuki YOSHIDA

University of Library and Information Science
1-2, Kasuga, Tsukuba-shi, Ibaraki-ken, 305, Japan

(Received : August 5, 1996 ; Accepted for publication : October 7, 1996)

The comparison algorithm of protein sequences by Murata was modified by considering only similarities between the same amino acid types and by introducing a lookup table. The modified algorithm calculates the similarity score between two protein sequences and aligns them. Computational times for calculating similarity scores against some proteins to all proteins in the Protein Sequence Database of the PIR by the system implementing our algorithm are about ten times shorter than those achieved by Murata. The alignments by our algorithm with a gap penalty of 18 are similar to those by Murata. The computational times by our system are two to three times slower, but the similarity scores are more sensitive than those by FASTA.

Keywords: alignment, similarity score, amino acid sequence, maximum array, lookup table

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