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. 2013:7:83-95.
doi: 10.4137/BBI.S11213. Epub 2013 Mar 7.

Computational small RNA prediction in bacteria

Jayavel Sridhar  1 , Paramasamy Gunasekaran
Affiliations

Computational small RNA prediction in bacteria

Jayavel Sridhar et al. Bioinform Biol Insights. 2013.

Abstract

Bacterial, small RNAs were once regarded as potent regulators of gene expression and are now being considered as essential for their diversified roles. Many small RNAs are now reported to have a wide array of regulatory functions, ranging from environmental sensing to pathogenesis. Traditionally, noncoding transcripts were rarely detected by means of genetic screens. However, the availability of approximately 2200 prokaryotic genome sequences in public databases facilitates the efficient computational search of those molecules, followed by experimental validation. In principle, the following four major computational methods were applied for the prediction of sRNA locations from bacterial genome sequences: (1) comparative genomics, (2) secondary structure and thermodynamic stability, (3) 'Orphan' transcriptional signals and (4) ab initio methods regardless of sequence or structure similarity; most of these tools were applied to locate the putative genomic sRNA locations followed by experimental validation of those transcripts. Therefore, computational screening has simplified the sRNA identification process in bacteria. In this review, a plethora of small RNA prediction methods and tools that have been reported in the past decade are discussed comprehensively and assessed based on their attributes, compatibility, and their prediction accuracy.

Keywords: base composition; comparative genomics; ncRNA; sRNA prediction; structure stability; transcriptional signal.

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Figures

Figure 1
Figure 1
(A) Comparative genomics based protocols utilized in the computational sRNA prediction tools: QRNA, ERPIN, ISI and RNAZ; (B) methodology adapted in the transcriptional signal-based sRNA finders: sRNAscanner and sRNAPredict; (C) sequence based ab initio sRNA detection methods: Atypical GC, RNAGENiE and smyRNA; (D) non-sequence based ab initio sRNA detection methods: PsRNA and NAPP. Abbreviations: IGR, InterGenic Region; sRNA, small RNA; rRNA, ribosomal RNA; tRNA, transfer RNA; CDS, Coding Domain Sequence; KO, KEGG Orthology; TFBS, Transcription Factor Binding Site.
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