Domain fusion analysis by applying relational algebra to protein sequence and domain databases.
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.uhnres.utoronto.ca/pi.


CONCLUSIONS
As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.
Truong
Kevin
K
Department of Medical Biophysics, University of Toronto, Toronto, M3N 1L6, Canada. ktruong@uhnres.utoronto.ca
Ikura
Mitsuhiko
M
D017398:Alternative Splicing / Q000235:genetics; D000818:Animals; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D030562:Databases, Protein / Q000706:statistics & numerical data; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics; D006801:Humans; D008432:Mathematical Computing; D011237:Predictive Value of Tests; D017434:Protein Structure, Tertiary / Q000235:genetics; D011995:Recombination, Genetic / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics; D029702:Schizosaccharomyces pombe Proteins / Q000737:chemistry / Q000235:genetics; D020539:Sequence Analysis, Protein / Q000379:methods / Q000706:statistics & numerical data*; D012984:Software
D029681:Arabidopsis Proteins; D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins