Skip Navigation



Bioinformatics Advance Access published online on January 25, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp013
This Article
Right arrow Advance Access manuscript (PDF)
Right arrow All Versions of this Article:
25/4/550    most recent
btp013v1
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 Blom, E.-J.
Right arrow Articles by van Hijum, S. A.F.T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Blom, E.-J.
Right arrow Articles by van Hijum, S. A.F.T.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Evert-Jan Blom a, Jos B.T.M. Roerdink b, Oscar P. Kuipers a,* and Sacha A.F.T. van Hijum a,c,*

aMolecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV, Groningen the Netherlands. bInstitute for Mathematics and Computing Science, University of Groningen, Nijenborgh 9, 9747 AG, Groningen the Netherlands. cCurrent address: NIZO Food Research, PO Box 20, 6710 BA Ede, the Netherlands.

*To whom correspondence should be addressed. E-mail: o.p.kuipers{at}rug.nlor sacha.vanhijum{at}nizo.nl


  Abstract

Summary: Unraveling regulatory mechanisms (e.g., identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cut-off and require additional manual processing steps. Our stand-alone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Availability: MOTIFATOR is freely available at http://www.motifator.nl

Contact: o.p.kuipers{at}rug.nl or sacha.vanhijum{at}nizo.nl

Supplementary information: details available at http://www.motifator.nl

Associate Editor: Dr. Joaquin Dopazo

Received on September 11, 2008; revised on November 19, 2008; accepted on January 1, 2009

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
 Microbiol. Mol. Biol. Rev.Home page
S. A. F. T. van Hijum, M. H. Medema, and O. P. Kuipers
Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation
Microbiol. Mol. Biol. Rev., September 1, 2009; 73(3): 481 - 509.
[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.