Bioinformatic Discovery of Bacterial Regulatory RNAs Using SIPHT

Part of the Methods in Molecular Biology book series (MIMB, volume 905)

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.

Key words

regRNA sRNA SIPHT Bioinformatics Annotation 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.The Broad Institute of MIT and HarvardCambridgeUSA
  2. 2.Channing LaboratoryBrigham and Women’s Hospital, Harvard Medical SchoolBostonUSA

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