Mocca: semi-automatic method for domain hunting

TitleMocca: semi-automatic method for domain hunting
Publication TypeJournal Article
Year of Publication2001
AuthorsNotredame C
JournalBioinformatics
Volume17
Pagination373-4
Date PublishedApr
Accession Number11301309
KeywordsAutomation, Databases, Factual, Information Storage and Retrieval, Protein Structure, Tertiary, Proteins/ analysis, Software
Abstract

MOTIVATION: Multiple OCCurrences Analysis (Mocca) is a new method for repeat extraction. It is based on the T-Coffee package (Notredame et al., JMB, 302, 205-217, 2000). Given a sequence or a set of sequences, and a library of local alignments, Mocca extracts every segment of sequence homologous to a pre-specified master. The implementation is meant for domain hunting and makes it fast and easy to test for new boundaries or extend known repeats in an interactive manner. Mocca is designed to deal with highly divergent protein repeats (less than 30% amino acid identity) of more than 30 amino acids.