MOTIF EXPLORER - A TOOL FOR INTERACTIVE EXPLORATION OF AMINOAC ID SEQUENCE MOTIFS

Short amino acid sequence patterns, call ed 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 enabl es 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 repetit ive searching and mot if description modification as motif exploration. In this paper , we discuss the application of generalized suffi x tree-based indexing structures to high performance motif exploration. We present Motif Explorer, a tool accessible via the World Wide Web capabl e of locating patterns in genet ic databases fast enough to support i nteractive exploration of sequence motifs.