Motif Explorer - a Tool for Interactive Exploration of Aminoacid Sequence Motifs

Short amino acid sequence patterns, called motifs, play an important role in molecular biology research. While a number of tools for locating motifs in sequence databases have been developed, no existing tool performs fast enough to allow interactive searching of entire databases. Interactive searching enables biologists to explore the effects of changes to a motif on the set of sequences matched by the motif. We refer to this process of repetitive searching and motif description modification as motif exploration. In this paper, we discuss the application of generalized suffix tree-based indexing structures to high performance motif exploration. We present Motif Explorer, a tool accessible via the World Wide Web capable of locating patterns in genetic databases fast enough to support interactive exploration of sequence motifs.