Approximate symbolic pattern matching for protein sequence data

In protein sequences, often two sequences that share similar substrings have similar functional properties. Learning of the characteristics and properties of an unknown protein is much easier if its likely functional properties can be predicted by finding the substrings already known from other protein sequences. The sequence pattern search algorithm proposed in this paper searches for similar matches between a pattern and a sequence by using fuzzy logic and calculates the degree of similarity from a sequence inference step. Proteins from 11 domain families are used for simulation and the result shows that the proposed algorithm is capable of identifying sequences that have a similar pattern compared to their family protein motifs. 2002 Elsevier Science Inc. All rights reserved.