target analysis

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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microRNA Target Prediction Tools

by Chris on November 16, 2009

in Web Based Tools

miRecords is resource for animal miRNA-target interactions developed at the University of Minnesota. miRecords consists of two components. The Validated Targets component is a large, high-quality database of experimentally validated miRNA targets resulting from meticulous literature curation. The Predicted Targets component of miRecords is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs

PicTar is an algorithm for the identification of microRNA targets. This searchable website provides details (3′ UTR alignments with predicted sites, links to various public databases etc) regarding microRNA target predictions in vertebrates, several Drosophila species, and C. elegans.

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander (miranda@cbio.mskcc.org).

TargetScan: Prediction of microRNA targets – These are the most recent TargetScanS predictions (April 2005). They are essentially the 3′UTR targets reported in the Lewis et al., 2005 paper, with a few changes arising from updated gene boundary definitions from the April 2005 UCSC genome browser mapping of RefSeq mRNAs to the hg17 human genome assembly. To avoid difficulties in browser display, the few predictions spanning splice junctions are excluded.   [click to continue…]

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