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

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. Availability and implementation The UEA sRNA Workbench is available at: http://srna-workbench.cmp.uea.ac.uk. The source code is available at: https://github.com/sRNAworkbenchuea/UEA_sRNA_Workbench Supplementary information Supplementary data are available at Bioinformatics online.

[1]  A. El-Osta,et al.  Evaluation of microRNA alignment techniques , 2016, RNA.

[2]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[3]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[4]  T. Chapman,et al.  Comparison of alternative approaches for analysing multi-level RNA-seq data , 2017, PloS one.

[5]  Matthew B. Stocks,et al.  CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data. , 2013, RNA biology.

[6]  Vincent Moulton,et al.  The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets , 2012, Bioinform..

[7]  Charlotte Soneson,et al.  A comparison of methods for differential expression analysis of RNA-seq data , 2013, BMC Bioinformatics.

[8]  J. Doudna,et al.  Molecular mechanisms of RNA interference. , 2013, Annual review of biophysics.

[9]  Peter M. Rice,et al.  The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants , 2009, Nucleic acids research.

[10]  Matthew B. Stocks,et al.  Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. , 2017, RNA.

[11]  Ping Xu,et al.  miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets , 2017, Bioinform..

[12]  Michael Hackenberg,et al.  sRNAtoolbox: an integrated collection of small RNA research tools , 2015, Nucleic Acids Res..