Skip Navigation

Nucleic Acids Research 2006 34(Web Server issue):W366-W368; doi:10.1093/nar/gkl069
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (49K) Freely available
Right arrow Screen PDF (50K) Freely available
Right arrow Alert me when this article is cited
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 arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Neph, S.
Right arrow Articles by Tompa, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Neph, S.
Right arrow Articles by Tompa, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes

Shane Neph and Martin Tompa*

Department of Computer Science and Engineering and Department of Genome Sciences, University of Washington Box 352350, Seattle, WA 98195-2350, USA

*To whom correspondence should be addressed. Tel: +1 206 543 9263; Fax: +1 206 543 8331; Email: tompa{at}cs.washington.edu

Received February 11, 2006. Revised February 19, 2006. Accepted March 1, 2006.

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of homologous regulatory regions, usually collected from multiple species. It does so by identifying the most conserved motifs in those homologous regions. This note describes web software that has been designed specifically for this purpose in prokaryotic genomes, making use of the phylogenetic relationships among the homologous sequences in order to make more accurate predictions. The software is called MicroFootPrinter and is available at http://bio.cs.washington.edu/software.html.


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]

Home page
 Brief BioinformHome page
J. Mrazek
Finding sequence motifs in prokaryotic genomes--a brief practical guide for a microbiologist
Brief Bioinform, September 1, 2009; 10(5): 525 - 536.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Z. Weinberg, J. E. Barrick, Z. Yao, A. Roth, J. N. Kim, J. Gore, J. X. Wang, E. R. Lee, K. F. Block, N. Sudarsan, et al.
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
Nucleic Acids Res., July 9, 2007; (2007) gkm487v1.
[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.