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PubMed · 2059850

A platform for biological sequence comparison on parallel computers.

A S Deshpande·D S Richards·W R Pearson
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Abstract

We have written two programs for searching biological sequence databases that run on Intel hypercube computers. PSCANLIB compares a single sequence against a sequence library, and PCOMPLIB compares all the entries in one sequence library against a second library. The programs provide a general framework for similarity searching; they include functions for reading in query sequences, search parameters and library entries, and reporting the results of a search. We have isolated the code for the specific function that calculates the similarity score between the query and library sequence; alternative searching algorithms can be implemented by editing two files. We have implemented the rapid FASTA sequence comparison algorithm and the more rigorous Smith-Waterman algorithm within this framework. The PSCANLIB program on a 16 node iPSC/2 80386-based hypercube can compare a 229 amino acid protein sequence with a 3.4 million residue sequence library in approximately 16 s with the FASTA algorithm. Using the Smith-Waterman algorithm, the same search takes 35 min. The PCOMPLIB program can compare a 0.8 million amino acid protein sequence library with itself in 5.3 min with FASTA on a third-generation 32 node Intel iPSC/860 hypercube.

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AlgorithmsAmino Acid SequenceDNAElectronic Data ProcessingGene LibrarySoftwareJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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BibTeXRIS

A S Deshpande, D S Richards, W R Pearson. 1991. A platform for biological sequence comparison on parallel computers.. https://doi.org/10.1093/bioinformatics%2F7.2.237

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