Literature DB >> 3753790

Sequence search on a supercomputer.

O Gotoh, Y Tagashira.   

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.

Entities:  

Mesh：

Year:  1986        PMID： 3753790      PMCID： PMC339355          DOI： 10.1093/nar/14.1.57

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  7 in total

1.  Optimal sequence alignments.

Authors:  W M Fitch; T F Smith
Journal:  Proc Natl Acad Sci U S A       Date:  1983-03       Impact factor: 11.205

2.  Nucleotide sequence and expression of an AIDS-associated retrovirus (ARV-2).

Authors:  R Sanchez-Pescador; M D Power; P J Barr; K S Steimer; M M Stempien; S L Brown-Shimer; W W Gee; A Renard; A Randolph; J A Levy
Journal:  Science       Date:  1985-02-01       Impact factor: 47.728

3.  Gene product of v-fgr onc: hybrid protein containing a portion of actin and a tyrosine-specific protein kinase.

Authors:  G Naharro; K C Robbins; E P Reddy
Journal:  Science       Date:  1984-01-06       Impact factor: 47.728

4.  Identification of common molecular subsequences.

Authors:  T F Smith; M S Waterman
Journal:  J Mol Biol       Date:  1981-03-25       Impact factor: 5.469

5.  An improved algorithm for matching biological sequences.

Authors:  O Gotoh
Journal:  J Mol Biol       Date:  1982-12-15       Impact factor: 5.469

6.  Rapid similarity searches of nucleic acid and protein data banks.

Authors:  W J Wilbur; D J Lipman
Journal:  Proc Natl Acad Sci U S A       Date:  1983-02       Impact factor: 11.205

7.  Platelet-derived growth factor is structurally related to the putative transforming protein p28sis of simian sarcoma virus.

Authors:  M D Waterfield; G T Scrace; N Whittle; P Stroobant; A Johnsson; A Wasteson; B Westermark; C H Heldin; J S Huang; T F Deuel
Journal:  Nature       Date:  1983 Jul 7-13       Impact factor: 49.962
  7 in total
  2 in total

1.  Optimized homology searches of the gene and protein sequence data banks.

Authors:  C B Lawrence; D A Goldman; R T Hood
Journal:  Bull Math Biol       Date:  1986       Impact factor: 1.758

2.  WImpiBLAST: web interface for mpiBLAST to help biologists perform large-scale annotation using high performance computing.

Authors:  Parichit Sharma; Shrikant S Mantri
Journal:  PLoS One       Date:  2014-06-30       Impact factor: 3.240
  2 in total

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