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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W109-13. doi: 10.1093/nar/gkn264. Epub 2008 May 13.

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

Author information

1
Computer Science Department, Wellesley College, Wellesley, MA 02481, USA. btjaden@wellesley.edu

Abstract

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.

PMID:
18477632
PMCID:
PMC2447797
DOI:
10.1093/nar/gkn264
[Indexed for MEDLINE]
Free PMC Article

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