Domain fusion analysis by applying relational algebra to protein sequence and domain databases.docVIP

BMC Bioinformatics BioMedCentral Methodology article Open Access Domain fusion analysis by applying relational algebra to protein sequence and domain databases Kevin Truong and Mitsuhiko Ikura* Address: Department of Medical Biophysics, University of Toronto, Toronto, M3N 1L6, Canada Email: Kevin Truong - ktruong@uhnres.utoronto.ca; Mitsuhiko Ikura* - mikura@uhnres.utoronto.ca * Corresponding author Published: 6 May 2003 Received: 25 February 2003 Accepted: 6 May 2003 BMC Bioinformatics 2003, 4:16 This article is available from: /1471-2105/4/16 ? 2003 Truong and Ikura; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the articles original URL. Abstract Background: Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results: This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS- PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnr