PRSS3  evaluates the significance of a protein sequence alignmentprss3 is used to evaluate the significance of a protein or DNA sequence similarity score by comparing two sequences and calculating optimal similarity scores, and then repeatedly shuffling the second sequence, and calculating optimal similarity scores using the SmithWaterman algorithm. An extreme value distribution is then fit to the shuffledsequence scores. The characteristic parameters of the extreme value distribution are then used to estimate the probability that each of the unshuffled sequence scores would be obtained by chance in one sequence, or in a number of sequences equal to the number of shuffles. This program is derived from rdf2, described by Pearson and Lipman, PNAS (1988) 85:24442448, and Pearson (Meth. Enz. 183:6398). Use of the extreme value distribution for estimating the probabilities of similarity scores was described by Altshul and Karlin, PNAS (1990) 87:22642268. The 'zvalues' calculated by rdf2 are not as informative as the Pvalues and expectations calculated by prdf. prss3 uses calculates optimal scores using the same rigorous SmithWaterman algorithm (Smith and Waterman, J. Mol. Biol. (1983) 147:195197) used by the ssearch3 program. prss3 also allows a more sophisticated shuffling method: residues can be shuffled within a local window, so that the order of residues 110, 1120, etc, is destroyed but a residue in the first 10 is never swapped with a residue outside the first ten, and so on for each local window. This program is part of the FASTA package of sequence analysis program.
