Scanning protein sequence databanks using a distributed processing workstation network

TY - JOUR

T1 - Scanning protein sequence databanks using a distributed processing workstation network

AU - Barton, G J

PY - 1991/1

Y1 - 1991/1

N2 - The programme pscan has been developed to distribute protein databank scans over a network of computers that share a common file system. pscan may be used in conjunction with most conventional sequence comparison programmes with few modifications. In test runs using the Smith-Waterman dynamic programming algorithm, the time required to scan a 6858 sequence databank using a query sequence 740 residues long was reduced from approximately 50 min for a single processor, to approximately 11 minutes for five processors. Accordingly, pscan provides a low-cost, portable alternative to dedicated parallel processing computers.

AB - The programme pscan has been developed to distribute protein databank scans over a network of computers that share a common file system. pscan may be used in conjunction with most conventional sequence comparison programmes with few modifications. In test runs using the Smith-Waterman dynamic programming algorithm, the time required to scan a 6858 sequence databank using a query sequence 740 residues long was reduced from approximately 50 min for a single processor, to approximately 11 minutes for five processors. Accordingly, pscan provides a low-cost, portable alternative to dedicated parallel processing computers.

KW - Algorithms

KW - Amino Acid Sequence

KW - Computer Communication Networks

KW - Genomic Library

KW - Programming Languages

KW - Proteins

KW - Software

U2 - 10.1093/bioinformatics/7.1.85

DO - 10.1093/bioinformatics/7.1.85

M3 - Article

C2 - 2004279

SN - 0266-7061

VL - 7

SP - 85

EP - 88

JO - Computer Applications in the Biosciences

JF - Computer Applications in the Biosciences

IS - 1

ER -