The identification of complete domains within protein sequences using accurate E-values for semi-global alignment.

ABSTRACT: The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the corresponding protein sequence. Ideally, complete domains are aligned to protein subsequences, in a 'semi-global alignment'. Local alignment, which aligns pieces of domains to subsequences, is common in high-throughput annotation applications, however. It is a mature technique, with the heuristics and accurate E-values required for screening large databases and evaluating the screening results. Hidden Markov models (HMMs) provide an alternative theoretical framework for semi-global alignment, but their use is limited because they lack heuristi

SUBMITTER: Kann MG 

PROVIDER: S-EPMC1950549 | biostudies-literature | 2007

REPOSITORIES: biostudies-literature