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Nucleic Acids Res. 2011 Aug;39(14):5845-52. doi: 10.1093/nar/gkr168. Epub 2011 Apr 7.

RNIE: genome-wide prediction of bacterial intrinsic terminators.

Author information

1
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, UK. pg5@sanger.ac.uk

Abstract

Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.

PMID:
21478170
PMCID:
PMC3152330
DOI:
10.1093/nar/gkr168
[Indexed for MEDLINE]
Free PMC Article

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