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Open Access Highly Accessed Software

GOmotif: A web server for investigating the biological role of protein sequence motifs

Franklin Bristow13, Runtao He12 and Gary Van Domselaar123*

Author Affiliations

1 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, R3E 3R2, Canada

2 Department of Medical Microbiology, School of Medicine, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada

3 Department of Computer Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada

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BMC Bioinformatics 2011, 12:379  doi:10.1186/1471-2105-12-379

Published: 26 September 2011

Abstract

Background

Many proteins contain conserved sequence patterns (motifs) that contribute to their functionality. The process of experimentally identifying and validating novel protein motifs can be difficult, expensive, and time consuming. A means for helping to identify in advance the possible function of a novel motif is important to test hypotheses concerning the biological relevance of these motifs, thus reducing experimental trial-and-error.

Results

GOmotif accepts PROSITE and regular expression formatted motifs as input and searches a Gene Ontology annotated protein database using motif search tools. The search returns the set of proteins containing matching motifs and their associated Gene Ontology terms. These results are presented as: 1) a hierarchical, navigable tree separated into the three Gene Ontology biological domains - biological process, cellular component, and molecular function; 2) corresponding pie charts indicating raw and statistically adjusted distributions of the results, and 3) an interactive graphical network view depicting the location of the results in the Gene Ontology.

Conclusions

GOmotif is a web-based tool designed to assist researchers in investigating the biological role of novel protein motifs. GOmotif can be freely accessed at http://www.gomotif.ca webcite