title: A platform for biological sequence comparison on parallel computers.
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.
authors.affiliation: Department of Computer Science, University of Virginia, Charlottesville 22908.
authors.forename: A S
authors.initials: AS
authors.lastname: Deshpande
authors.forename: D S
authors.initials: DS
authors.lastname: Richards
authors.forename: W R
authors.initials: WR
authors.lastname: Pearson
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D004247:DNA / Q000032:analysis*; D001330:Electronic Data Processing; D015723:Gene Library; D012984:Software
chemical_list: D004247:DNA