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Bioinformatics. 2012 Aug 1;28(15):2059-61. doi: 10.1093/bioinformatics/bts311. Epub 2012 May 24.

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

Author information

1
School of Computing Sciences, University of East Anglia, Norwich Research Park, NR4 7TJ, Norwich, UK.

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.

AVAILABILITY:

The program and help pages are available at http://srna-workbench.cmp.uea.ac.uk.

CONTACT:

vincent.moulton@cmp.uea.ac.uk.

PMID:
22628521
PMCID:
PMC3400958
DOI:
10.1093/bioinformatics/bts311
[Indexed for MEDLINE]
Free PMC Article

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