Skip Navigation



Nucleic Acids Research Advance Access published online on May 13, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn264
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (4047K) Freely available
Right arrow Screen PDF (539K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_2/W109    most recent
gkn264v1
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 Tjaden, B.
PubMed
Right arrow PubMed Citation
Right arrow Articles by Tjaden, B.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Web Server Issue

TargetRNA: a tool for predicting targets of small RNA action in bacteria

Brian Tjaden*

Computer Science Department, Wellesley College, Wellesley, MA 02481, USA

*To whom correspondence should be addressed. Tel: +1 781 283 3354; Fax: +1 781 283 3642; Email: btjaden{at}wellesley.edu

Received January 31, 2008. Revised April 11, 2008. Accepted April 21, 2008.

Many small RNA (sRNA) genes in bacteria act as posttranscriptional regulators of target messenger RNAs. Here, we present TargetRNA, a web tool for predicting mRNA targets of sRNA action in bacteria. TargetRNA takes as input a genomic sequence that may correspond to an sRNA gene. TargetRNA then uses a dynamic programming algorithm to search each annotated message in a specified genome for mRNAs that evince basepair-binding potential to the input sRNA sequence. Based on the calculated basepair-binding potential of each message with the given sRNA regulator, TargetRNA outputs a ranked list of candidate mRNA targets along with the predicted basepairing interaction of each target to the sRNA. The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA.


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




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.