Skip Navigation



Bioinformatics Advance Access published online on March 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn105
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
24/10/1307    most recent
btn105v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Edwards, R. J.
Right arrow Articles by Shields, D. C.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Edwards, R. J.
Right arrow Articles by Shields, D. C.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CompariMotif: Quick and easy comparisons of sequence motifs

Richard J. Edwards *,1,2, Norman E. Davey 1 and Denis C. Shields 1

1 UCD Complex and Adaptive Systems Laboratory and UCD Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland. 2 School of Biological Sciences, University of Southampton, Boldrewood Campus, Southampton SO167PX.

*To whom correspondence should be addressed. Dr. Richard J. Edwards, E-mail: r.edwards{at}southampton.ac.uk


  Abstract

Summary: CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs, and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs.

Availability: CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available under a GNU GPL from http://bioinformatics.ucd.ie/shields/software/comparimotif/.

Contact: r.edwards{at}southampton.ac.uk

Supplementary information: Further details are available at http://bioinformatics.ucd.ie/shields/software/comparimotif/.

Associate Editor: Prof. Burkhard Rost

Received on February 11, 2008; revised on March 18, 2008; accepted on March 19, 2008

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
D. T.-H. Chang, T.-Y. Chien, and C.-Y. Chen
seeMotif: exploring and visualizing sequence motifs in 3D structures
Nucleic Acids Res., July 1, 2009; 37(suppl_2): W552 - W558.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. S. Keshava Prasad, R. Goel, K. Kandasamy, S. Keerthikumar, S. Kumar, S. Mathivanan, D. Telikicherla, R. Raju, B. Shafreen, A. Venugopal, et al.
Human Protein Reference Database--2009 update
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D767 - D772.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.