Sequence search on a supercomputer | Zendy

Osamu Gotoh | Zendy; Yusaku Tagashira | Zendy

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Sequence search on a supercomputer

Author(s) -

Osamu Gotoh,

Yusaku Tagashira

Publication year - 1986

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/14.1.57

Subject(s) - supercomputer , genbank , sequence database , fortran , sequence (biology) , biology , uniprot , parallel computing , computer science , base (topology) , computational biology , bioinformatics , computational science , operating system , genetics , mathematics , gene , mathematical analysis

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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