A Platform for Biological Sequence Comparison on Parallel ComputersReport
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 pararneters, 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 about 16 seconds with the FASTA algorithm. Using the Smith-Waterman algorithm, the same search takes 35 minutes. The PCOMPLIB program can compare a 0.8 million amino acid protein sequence library with itself in 5.3 minutes with FASTA on a third-generation 32»node Intel iPSC/860 hypercube.
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Deshpande, A, and D Richards. "A Platform for Biological Sequence Comparison on Parallel Computers." University of Virginia Dept. of Computer Science Tech Report (1990).
University of Virginia, Department of Computer Science