SECOM: a novel hash seed and community detection based-approach for genome-scale protein domain identification.

ABSTRACT: With rapid advances in the development of DNA sequencing technologies, a plethora of high-throughput genome and proteome data from a diverse spectrum of organisms have been generated. The functional annotation and evolutionary history of proteins are usually inferred from domains predicted from the genome sequences. Traditional database-based domain prediction methods cannot identify novel domains, however, and alignment-based methods, which look for recurring segments in the proteome, are computationally demanding. Here, we propose a novel genome-wide domain prediction method, SECOM. Instead of conducting all-against-all sequence alignment, SECOM first indexes all the proteins in the genome by using a hash seed function. Local similarity can thus be detected and encoded into a graph struc

SUBMITTER: Fan M 

PROVIDER: S-EPMC3386278 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature