title: Protein domain identification and improved sequence similarity searching using PSI-BLAST.
abstract: Protein sequences containing more than one structural domain are problematic when used in homology searches where they can either stop an iterative database search prematurely or cause an explosion of a search to common domains. We describe a method, DOMAINATION, that infers domains and their boundaries in a query sequence from local gapped alignments generated using PSI-BLAST. Through a new technique to recognize domain insertions and permutations, DOMAINATION submits delineated domains as successive database queries in further iterative steps. Assessed over a set of 452 multidomain proteins, the method predicts structural domain boundaries with an overall accuracy of 50% and improves finding distant homologies by 14% compared with PSI-BLAST. DOMAINATION is available as a web based tool at http://mathbio.nimr.mrc.ac.uk, and the source code is available from the authors upon request.
authors.affiliation: Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, United Kingdom.
authors.forename: Richard A
authors.initials: RA
authors.lastname: George
authors.forename: Jaap
authors.initials: J
authors.lastname: Heringa
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D020449:Repetitive Sequences, Amino Acid; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins