An Efficient Exact Algorithm for the Motif Stem Search Problem over Large Alphabets

• Published in: IEEE/ACM transactions on computational biology and bioinformatics Vol. 12; no. 2; pp. 384 - 397
• Main Authors: Qiang Yu, Hongwei Huo, Vitter, Jeffrey Scott, Jun Huan, Nekrich, Yakov
• Format: Journal Article
• Language: English
• Published: United States IEEE 01.03.2015; The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Subjects: Algorithm design and analysis; Algorithms; Alphabets; Amino Acid Motifs; Bioinformatics; Biology; Computational biology; Computational Biology - methods; Computer Simulation; Construction; Hamming distance; Motif stem search; pattern driven; Pattern Recognition, Automated - methods; Proteins - chemistry; Radiation detectors; regular expressions; Searching; Segments; Sequence Analysis, Protein - methods; Strings; regular expressions; pattern driven; Motif stem search
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2014.2361668

In recent years, there has been an increasing interest in planted (l, d) motif search (PMS) with applications to discovering significant segments in biological sequences. However, there has been little discussion about PMS over large alphabets. This paper focuses on motif stem search (MSS), which is recently introduced 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, and the superset is expected to be as small as possible. 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 method for generating all possible motif stems without redundant wildcards. (3) We propose an efficient exact algorithm, called StemFinder, for solving the MSS problem. Compared with the previous MSS algorithms, StemFinder runs much faster and reports fewer stems which represent a smaller superset of all (l, d) motifs. StemFinder is freely available at http://sites.google.com/site/feqond/stemfinder.