The UEA sRNA workbench: A suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets

Matthew B. Stocks, Simon Moxon, Daniel Mapleson, Hugh C. Woolfenden, Irina Mohorianu, Leighton Folkes, Frank Schwach, Tamas Dalmay, Vincent Moulton*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

203 Citations (Scopus)

Abstract

Summary: RNA silencing is a complex, highly conserved mechanism mediated by small RNAs (sRNAs), such as microRNAs (miRNAs), that is known to be involved in a diverse set of biological functions including development, pathogen control, genome maintenance and response to environmental change. Advances in next generation sequencing technologies are producing increasingly large numbers of sRNA reads per sample at a fraction of the cost of previous methods. However, many bioinformatics tools do not scale accordingly, are cumbersome, or require extensive support from bioinformatics experts. Therefore, researchers need user-friendly, robust tools, capable of not only processing large sRNA datasets in a reasonable time frame but also presenting the results in an intuitive fashion and visualizing sRNA genomic features. Herein, we present the UEA sRNA workbench, a suite of tools that is a successor to the web-based UEA sRNA Toolkit, but in downloadable format and with several enhanced and additional features.

Original languageEnglish
Article numberbts311
Pages (from-to)2059-2061
Number of pages3
JournalBioinformatics
Volume28
Issue number15
DOIs
Publication statusPublished - Aug 2012
Externally publishedYes

Bibliographical note

Funding Information:
Funding: Biotechnology and Biological Sciences Research Council (grant BBSRC BB/I00016X/1).

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