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Methods Mol Biol DOI:10.1007/978-1-61779-949-5_1

Bioinformatic discovery of bacterial regulatory RNAs using SIPHT.

Publication TypeJournal Article
Year of Publication2012
AuthorsLivny, J
JournalMethods Mol Biol
Volume905
Pages3-14
Date Published2012
ISSN1940-6029
KeywordsComputational Biology, Genetic Loci, Internet, Molecular Sequence Annotation, Regulatory Sequences, Ribonucleic Acid, Replicon, RNA, Bacterial, Software
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.

URLhttp://dx.doi.org/10.1007/978-1-61779-949-5_1
DOI10.1007/978-1-61779-949-5_1
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/22735994?dopt=Abstract

Alternate JournalMethods Mol. Biol.
PubMed ID22735994