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Bioinformatics Advance Access published online on August 19, 2008
Bioinformatics, 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,*, Frank Schwach 1,*, Dan MacLean 2, Tamas Dalmay 1, David J Studholme 2 and Vincent Moulton 1

1University of East Anglia, Norwich, NR4 7TJ, UK.
2The Sainsbury Laboratory, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.

*To whom correspondence should be addressed. Vincent Moulton, E-mail: vincent.moulton{at}cmp.uea.ac.uk


  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@cmp.uea.ac.uk

*These authors contributed equally to this work

Associate Editor: Ivo Hofacker

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

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