Domain identification by clustering sequence alignments

Motivation: As sequence databases grow rapidly results from sequence compar ison searches using fast search methods such as BLAST and FASTA tend to be long and difficult to digest. Results: In this paper, we present a new method to extract domain informati on from sequence comparison searches by clustering the resulting alignments according to their similarity to the query sequence. Efficient tree struct ures and algorithms are used to organize the alignment data such that struc turally conserved elements can be easily identified. The hierarchical natur e of the data structures used and the flexible X-Window-based interface pro vide an efficient and intuitive means to explore the alignment data at diff erent levels so that the common domains, as well as distantly related featu res, can be explored.