A Consensus Algorithm for Simple Motifs Finding

In this paper, we are interested in the problem of finding patterns in strings coding biological macromolecules. We are, particularly, interested in the Simple Motif Search Problem (SMP). We propose a new algorithm to process this problem called SMS_H_CCA, which allows searching the most specific patterns and therefore the most relevant ones to biologists. This algorithm is based on the use of a hash table of patterns as an indexing structure, and the search for the approximate consensus strings. SMS_H_CCA makes use of less time and space than the known algorithms dealing with SMP.