Posted Fri, Mar, 08,2013
Published today in Bioinformatics and Biology Insights is a new review article by Jayavel Sridhar and Paramasamy Gunasekaran. Read more about this paper below:
Title
Computational Small RNA Prediction in Bacteria
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.
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Interview with Professor Jamie DaviesAs Editor-in-Chief of Biomarkers in Cancer I wanted to know what it is like to publish in my own journal. I have already published over 70 papers, so I knew what a range of other journals were like. I was impressed by the quality of the reviewers comments which made the paper so much better before it was accepted for publication. I was pleasantly surprised by how quickly the article went from acceptance to published, ...
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