Automated protein sequence database classification: II. Delineation of domain boundaries from sequence similarities

Abstract

Motivation: Decomposing each protein into modular domains is a basic prerequisite to classify accurately structural units in biological molecules. Boundaries between domains are indicated by two similar amino acid sequence segments located within the same protein (repeats) or within homologous proteins at notably different distances from their respective N- or C-termini. Results: We have developed an automated method that combines such positional constraints derived from various detected pairwise sequence similarities to delineate the modular organisation of proteins. The procedure has been applied to a non-redundant data set of 26,990 proteins whose sequences were taken from the PIR and SWISS-PROT databanks and shared < 60% sequence identity amongst pairs. The resultant clustering, delineation and multiple alignment of 24,380 sequence fragments yielded a new database of 4364 domain families. Comparison of the domain collection with that of PRODOM indicates a clear improvement in the number and size of domain families, domain boundaries and multiple sequence alignments. The accuracy and sinsitivity of the method are illustrated by results obtained for ankyrin-like repeats and EGF-like modules. Availability: The resulting database, called DOMO, is available through the database search routine SRS at Infobiogen (http://www.infobiogen.fr/srs5/), EBI (http://srs.ebi.ac.uk:5000/) and EMBL (http://www.embl-heidelberg.de/srs5/) World Wide Web sites. Contact: gracy@@@infobiogen.fr.