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Bioinformatics Advance Access originally published online on August 19, 2008
Bioinformatics 2008 24(19):2252-2253; doi:10.1093/bioinformatics/btn428
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A toolkit for analysing large-scale plant small RNA datasets

Simon Moxon 1,{dagger}, Frank Schwach 1,{dagger}, Tamas Dalmay 2, Dan MacLean 3, David J. Studholme 3 and Vincent Moulton 1,*

1School of Computing Sciences, 2School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ and 3The Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UK

*To whom correspondence should be addressed.


  Abstract

Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci.

Availability: The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk

Contact: vincent.moulton{at}cmp.uea.ac.uk

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Associate Editor: Ivo Hofacker

Received on May 27, 2008; revised on July 14, 2008; accepted on August 10, 2008

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