Bioinformatic discovery of bacterial regulatory RNAs using SIPHT.

Methods Mol Biol
Authors
Keywords
Abstract

Diverse bacteria encode RNAs that are not translated into proteins but are instead involved in regulating a wide variety of cellular functions. Computational approaches have proven successful in identifying numerous regulatory RNAs in myriad bacterial species but the difficultly of implementing most of these approaches has limited their accessibility to many researchers. Moreover, few of these approaches provide annotations of predicted loci to guide downstream experimental validation and characterization. Here I describe the implementation of SIPHT, a web-accessible program that enables screens for putative loci encoding regulatory RNAs to be conducted in any of nearly 2,000 sequenced bacterial replicons. SIPHT identifies candidate loci by searching for regions of intergenic sequence conservation upstream of predicted intrinsic transcription terminators. Each locus is then annotated for numerous features that provide clues about its potential function and/or enable the most reliable candidates to be identified.

Year of Publication
2012
Journal
Methods Mol Biol
Volume
905
Pages
3-14
Date Published
2012
ISSN
1940-6029
URL
DOI
10.1007/978-1-61779-949-5_1
PubMed ID
22735994
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