Sequence search on a supercomputer.

O Gotoh; Y Tagashira

doi:10.1093/nar/14.1.57

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Sequence search on a supercomputer.

O Gotoh·Y Tagashira

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Abstract

A set of programs was developed for searching nucleic acid and protein sequence data bases for sequences similar to a given sequence. The programs, written in FORTRAN 77, were optimized for vector processing on a Hitachi S810-20 supercomputer. A search of a 500-residue protein sequence against the entire PIR data base Ver. 1.0 (1) (0.5 M residues) is carried out in a CPU time of 45 sec. About 4 min is required for an exhaustive search of a 1500-base nucleotide sequence against all mammalian sequences (1.2M bases) in Genbank Ver. 29.0. The CPU time is reduced to about a quarter with a faster version.

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Amino Acid Sequence Base Sequence Computers Information Systems Software Time Factors Journal Article Research Support, Non-U.S. Gov't

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O Gotoh, Y Tagashira. 1986-01-10. Sequence search on a supercomputer.. https://doi.org/10.1093/nar%2F14.1.57

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