Computational techniques for motif search

Abstract

In the study of protein-protein interactions, one is interested in identifying domains as well as short motifs that bind to these domains. Short motifs also confer functions to proteins such as post-translational modification, protein-protein interaction, and protein trafficking. Identification of domains is relatively easy since they are sufficiently long enough to render the likelihood of occurrences by random chance very low. On the other hand, the identification of motifs is a challenge since they are typically very short. Thus it is vital to develop efficient techniques to identify motifs. In this paper we survey some of the techniques that have been proposed in the literature for motifs identification.