The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs

Stocks, Matthew B., Mohorianu, Irina, Beckers, Matthew, Paicu, Claudia, Moxon, Simon, Thody, Joshua, Dalmay, Tamas and Moulton, Vincent (2018) The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs. Bioinformatics, 34 (19). 3382–3384. ISSN 1367-4803

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Abstract

Motivation: RNA interference, a highly conserved regulatory mechanism, is mediated via small RNAs (sRNA). Recent technical advances enabled the analysis of larger, complex datasets and the investigation of microRNAs and the less known small interfering RNAs. However, the size and intricacy of current data requires a comprehensive set of tools, able to discriminate the patterns from the low-level, noise-like, variation; numerous and varied suggestions from the community represent an invaluable source of ideas for future tools, the ability of the community to contribute to this software is essential. Results: We present a new version of the UEA sRNA Workbench, reconfigured to allow an easy insertion of new tools/workflows. In its released form, it comprises of a suite of tools in a user-friendly environment, with enhanced capabilities for a comprehensive processing of sRNA-seq data e.g. tools for an accurate prediction of sRNA loci (CoLIde) and miRNA loci (miRCat2), as well as workflows to guide the users through common steps such as quality checking of the input data, normalization of abundances or detection of differential expression represent the first step in sRNA-seq analyses.

Item Type: Article
Faculty \ School: Faculty of Science > School of Computing Sciences
Faculty of Science > School of Biological Sciences
Depositing User: Pure Connector
Date Deposited: 25 Apr 2018 10:31
Last Modified: 18 Mar 2020 01:19
URI: https://ueaeprints.uea.ac.uk/id/eprint/66827
DOI: 10.1093/bioinformatics/bty338

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