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Nucleic Acids Research Advance Access originally published online on May 13, 2008
Nucleic Acids Research 2008 36(Web Server issue):W109-W113; doi:10.1093/nar/gkn264
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W109-W113
© 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.

Articles

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.


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A. Busch, A. S. Richter, and R. Backofen
IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
Bioinformatics, December 15, 2008; 24(24): 2849 - 2856.
[Abstract] [Full Text] [PDF]


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