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

BMC Bioinformatics

Software

Franklin Bristow¹  Runtao He²  Gary Van Domselaar³ 

[1] National Microbiology Laboratory, Public Health Agency of Canada, R3E 3R2, Winnipeg, MB, Canada;Department of Computer Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada;National Microbiology Laboratory, Public Health Agency of Canada, R3E 3R2, Winnipeg, MB, Canada;Department of Medical Microbiology, School of Medicine, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada;National Microbiology Laboratory, Public Health Agency of Canada, R3E 3R2, Winnipeg, MB, Canada;Department of Medical Microbiology, School of Medicine, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada;Department of Computer Science, University of Manitoba, R3T 2N2, Winnipeg, MB, Canada;

关键词: Gene Ontology;    Zinc Finger Motif;    Motif Search;    SwissProt Database;    Tree View;   

DOI  :  10.1186/1471-2105-12-379

 received in 2011-05-17, accepted in 2011-09-26,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundMany 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.ResultsGOmotif 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.ConclusionsGOmotif 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

【 授权许可】

Unknown   
© Bristow et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.