Software

The UEA small RNA Workbench is a suite of tools for analyzing micro RNA and other small RNA data from High-Throughput Sequencing devices.  For a quick overview of what the UEA sRNA Workbench can do for you, and which tool you should select for the task, please visit this page.

Latest release is version 4.2 alpha which is released as java binaries only to streamline the release process until the software moves into the stable release stage of its lifecycle.

Download 4.2 alpha

Changes include:

General

  1. All linux binaries are now compiled as 64bit removing the need to install the 32bit libraries prior to running the software
  2. Bug fixes and stability improvements

miRCat 1 (Version 3.2)

  1. Fixed the show genome browser view

RNA Annotation

  1. Fixed the issues with hairpin sequences not rendering

VisSR

  1. Fixed the issues with the VisSR tool not having required resources included within the most recent build

Database

  1. Chromosome headers can now be much longer than in previous versions (very long chromosome headers such as those found in scaffolded files caused the software to crash)

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miRWalk 2.0 available

by Christoph on December 2, 2014

in Software, Web Based Tools

miRWalk-2-logomiRWalk2.0 (http://zmf.umm.uni-heidelberg.de/apps/zmf/mirwalk2/) which is a significantly improved and upgraded version of miRWalk database is now available for the scientific community.

miRWalk2.0 was developed with the aim of providing a regularly updated, freely accessible, comprehensive archive to supply the biggest available collection of predicted and experimentally verified miRNA-target interactions with various novel and unique features to greatly assist the scientific community. About 858,750,070 interactions between 11,748 miRNAs and 308,700 genes are documented in miRWalk2.0 with 5,077,757 different kinds of identifiers to offer a one-stop site to collect an abundance of information.

miRWalk2.0 not only documents miRNA binding sites within the complete sequence of a gene, but also combines this information with a comparison of binding sites [click to continue…]

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starBase v2.0 logostarBase v2.0 update available

starBase is a database that can be used for decoding miRNA-mRNA, miRNA-ceRNA, miRNA-lncRNA, miRNA-circRNA, miRNA-pseudogene and protein-RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. starBase v2.0 now also provides visualization, analysis, discovery and downloading of above-mentioned large-scale functional genomics data.

Currently, starBase v.20 includes (1)108 CLIP-Seq datasets, (2)~500,000 miRNA-mRNA interactions, (3)~10,000 miRNA-lncRNA interactions(4)~16,000 miRNA-pseudogene interactions, (5)~9,000 miRNA-circRNA interactions, (6)~10,000 ceRNA pairs, (7)~300,000 protein-RNA interactions, (8) two tools for functional annotation from ceRNA and miRNA regulatory networks.
starBase v2.0 is freely available at http://starbase.sysu.edu.cn/.

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The UEA sRNA Workbench is a collection of software tools specifically designed to identify and analyze features in small RNA data. Yesterday, the Alpha release of The UEA Small RNA Workbench Version 3.0 was announced.  This release includes a brand new tool for general small RNA locus detection called CoLIde. For more information and  some changes to existing tools please see the following page for further details.

A stable release can be expected  as soon as possible and will include further changes to other areas of the Workbench. When the stable release is available the final version code of the software will change to 3.0

Download 3.0 (Alpha)

For the less adventurous: latest stable release is version 2.5.0 (Dec. 13th 2012) which can be found here:

Download 2.5.0 (Stable Release)

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The latest update (Aug. 14th 2012) covers  changes to the behavior of some tools in the Workbench, includes the usual bug fixes, as well as small re-branding of the software suite. As part of the later, The UEA sRNA Workbench will now be referred to as The UEA Small RNA Workbench.

The UEA Small RNA Workbench is a downloadable sRNA software package of tools specifically designed to identify and analyze features in small RNA data. This includes:

Preparation of sRNA data

  • Adapter Removal tool to strip adapter fragments from sequencing data.
  • Filter tool for further filtering to remove sequences that are of no interest to the user.

Aligning sRNA Data to a long read file such as a Genome

Analysing small RNA data

The UEA sRNA Workbench can perform various types of analysis on prepared small RNA data taken from Next Generation Sequencing experiments. The tool you use for analysis depends on what information you wish to extract from your data. The following list gives a short detail on each analysis type and a link to the tool you should use for this analysis.

  • Predicting novel miRNA sequences – miRCat
  • Determine normalised expression levels of miRNA sequences found in miRBase from multiple input samples – miRProf
  • Compare sRNA expression levels from multiple input samples – SiLoCo
  • Predicting phased ta-siRNAs in plant datasets – ta-si Prediction
  • Degradome assisted miRNA target prediction – PAREsnip

Visualising small RNA data and results

  • RNA Annotation tool to generate secondary structure plots of RNA sequences.
  • VisSR tool to browse genome files and their associated GFF records containing gene annotations. Alternatively this tool can be used for viewing sRNA alignments taken directly from the Sequence Alignment tool.

And as always: don’t forget to cite the tools you use: http://srna-workbench.cmp.uea.ac.uk/how-to-cite-us/

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sRNA Workbench Version 2.3.2 Released

April 12, 2012

The sRNA Workbench is a Java based suite of tools for analyzing small RNA/miRNA data from Next Generation Sequencing devices. Latest version is 2.3.2 and was released yesterday. The update covers several bug fixes and behavior modifications relating to all operating systems and several tools. sRNA Workbench home page: http://srna-workbench.cmp.uea.ac.uk/ Direct download link: http://sourceforge.net/projects/srnaworkbench/ Changes […]

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

March 8, 2012

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 […]

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miRvar: Database for Genomic Variations in microRNAs

October 19, 2011

The regulatory role of microRNAs (miRNAs) has been well studied in a wide variety of biological processes but there have been litle systematic efforts to understand and analyze the genetic variations in miRNA loci and study its functional consequences. Vinod Scaria’s group at the Institute of Genomics and Integrative Biology (CSIR) in Delhi comprehensively curated […]

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MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

May 10, 2011

MiRPara was developed as an effective tool for locating miRNAs coding regions in genome sequences and can be used as a screening step prior to HTS experiments. Goal is to predict most probable mature miRNA coding regions from genome scale sequences in a species specific manner. The authors classified sequences from miRBase into animal, plant […]

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miRNAkey – A software pipeline for the analysis of microRNA Deep Sequencing data

September 13, 2010

Deep Sequencing technologies (Next Generation Sequencing) are increasingly used to obtain a more accurate depiction of miRNA expression profiles in living cells. This type of analysis is a key step towards improving our understanding of the complexity and mode of miRNA regulation. miRNAkey is a software package designed by Researchers at Tel Aviv University and […]

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