StemFinder: An efficient algorithm for searching motif stems over large alphabets

Motif stem search (MSS) is a recent motif search problem to search motifs on large-alphabet inputs. A motif stem is an l-length string with some wildcards. The goal of the MSS problem is to find a set of stems that represents a superset of all (l, d) motifs present in the input sequences. The three main contributions of this paper are as follows: (1) We build motif stem representation more precisely by using regular expressions. (2) We give a new method for generating all possible motif stems. (3) We propose an efficient algorithm, called StemFinder, for solving the MSS problem. Compared with the previous algorithms, StemFinder runs much faster and first solves the (17, 8), (19, 9) and (21, 10) challenging instances on protein sequences; moreover, StemFinder reports fewer stems representing a smaller superset of all (l, d) motifs.