Study of protein sequence comparison metrics on the connection machine CM-2 |
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| Authors: | Eric Lander Jill P Mesirov Washington Taylor IV |
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| Affiliation: | (1) Whitehead Institute for Biomedical Research, 9 Cambridge Center, 02142 Cambridge, Massachusetts, USA;(2) Harvard University, 02138 Cambridge, Massachusetts, USA;(3) Thinking Machines Corporation, 245 First Street, 02142-1214 Cambridge, Massachusetts, USA |
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| Abstract: | Software tools have been developed to do rapid, large-scale protein sequence comparisons on databases of amino acid sequences, using a data parallel computer architecture. This software enables one to compare a protein against a database of several thousand proteins in the same time required by a conventional computer to do a single protein-protein comparison, thus enabling biologists to find relevant similarities much more quickly, and to evaluate many different comparison metrics in a reasonable period of time. We have used this software to analyze the effectiveness of various scoring metrics in determining sequence similarity, and to generate statistical information about the behavior of these scoring systems under the variation of certain parameters.An earlier version of this paper was presented at Supercomputing '88.Eric Lander was supported in part by National Science Foundation grant #NSF-DCB-8611317 and System Development Foundation grant #SDF612 |
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| Keywords: | proteins sequence comparison dynamic programming parallel computing computational biology |
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