Study of protein sequence comparison metrics on the Connection Machine CM-2

Software tools have been developed to perform rapid large-scale protein sequence comparisons on databases of amino-acid sequences, using a data-parallel computer architecture. This software makes it possible 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. This software was used 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