PMID:16717284

Citation	Tjaden, B, Goodwin, SS, Opdyke, JA, Guillier, M, Fu, DX, Gottesman, S and Storz, G (2006) Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res. 34:2791-802
Abstract	Many small, noncoding RNAs in bacteria act as post-transcriptional regulators by basepairing with target mRNAs. While the number of characterized small RNAs (sRNAs) has steadily increased, only a limited number of the corresponding mRNA targets have been identified. Here we present a program, TargetRNA, that predicts the targets of these bacterial RNA regulators. The program was evaluated by assessing whether previously known targets could be identified. The program was then used to predict targets for the Escherichia coli RNAs RyhB, OmrA, OmrB and OxyS, and the predictions were compared with changes in whole genome expression patterns observed upon expression of the sRNAs. Our results show that TargetRNA is a useful tool for finding mRNA targets of sRNAs, although its rate of success varies between sRNAs.
Links	PubMed PMC1464411 Online version:10.1093/nar/gkl356
Keywords	Base Pairing; Base Sequence; Computational Biology; Escherichia coli/genetics; Escherichia coli/metabolism; Gene Expression Regulation, Bacterial; Internet; Molecular Sequence Data; RNA, Bacterial/chemistry; RNA, Messenger/chemistry; RNA, Messenger/metabolism; RNA, Untranslated/chemistry; Software
edit table

Significance

You can help EcoliWiki by summarizing why this paper is useful

You can help Ecoliwiki by describing the useful materials (strains, plasmids, antibodies, etc) described in this paper.

Add links to pages that link here (e.g. gene, product, method pages)

See Help:References for how to manage references in EcoliWiki.