Java based sRNA workbench for analysing small RNA data from Next Generation Sequencing devices

by Christoph on March 8, 2012

in Software

The UEA sRNA workbench was developed by the Moulton group at the University of East Anglia and is a new simple to use, downloadable, Java based sRNA software package. It is based on algorithms developed for the 2008 released original UEA sRNA Toolkit. The software will perform a complete analysis of single or multiple-sample sRNA datasets from both plants and animals to identify interesting landmarks (such as detection of novel miRNA sequences) in genetic data. The latest Version 2.3.1 (Released: March 9th 2012) includes now the PAREsnip tool which allows to find targets of small RNAs using the degradome. For more see the PAREsnip page.

Currently, the downloadable version of the UEA sRNA workbench contains a subset of the web-based sRNA toolkit functionality. The later is still available for animal as well as plant and both version can be accessed from the main UEA sRNA toolkit site.

The UEA sRNA workbench is available for download at: srna-workbench.cmp.uea.ac.uk

citation for the original version:
S. Moxon, F. Schwach, D. MacLean, T. Dalmay, D. J Studholme, and V. Moulton
A toolkit for analysing large-scale plant small RNA datasets. 
Bioinformatics
 2008

http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn428

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