Looking to analyze small RNA data? Look no further than the sRNA Workbench. Developed by the esteemed UEA sRNA Workbench Team, this comprehensive software gives you the tools to identify, quantify, and visualize small RNA sequences with ease. With an intuitive interface and cutting-edge algorithms, the sRNA Workbench is a must-have for anyone working with small RNA data. Download it today and see the difference it can make for your research.

sRNA silencing is a complex, highly-conserved, transcriptional and post-transcriptional mechanism that tunes gene expression. RNA silencing is mediated by molecules known as small RNAs (sRNAs). Well-known examples of sRNAs include short-interfering RNA (siRNA), microRNAs (miRNAs), trans-acting short-interfering RNA (tasi-RNA) and Piwi-interacting RNA (piRNA). It was originally studied as a defence mechanism against pathogens in plants and later studied extensively due to its ability to regulate cancer-related genes.

The UEA sRNA workbench is a new simple to use, downloadable sRNA software package based on algorithms developed for the original UEA sRNA Toolkit that 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.

A complete list of the functionality offered in the UEA sRNA Workbench and detailed help on each tool can be found at the tools pages. Alternatively, an extensive help menu is available from the sRNA Workbench when running in GUI mode.

Features:

Adaptor Remover: removes adaptor fragments from raw short read sequence data and outputs data to FASTA format.
Filter: produces a filtered version of an sRNA dataset, controlled by several user-defined criteria, including sequence length, abundance, complexity, transfer and ribosomal RNA removal.
miRCat2 (miRNA Categorisation): predicts mature miRNAs and their precursors from an sRNA dataset and a genome.
SiLoCo (Short interfering RNA Locus Comparison): compares sRNA expression levels in multiple samples by grouping sRNAs into loci based on genomic location
ta-siRNA (trans-acting short interfering RNA): prediction of phased ta-siRNAs in plant sRNA datasets.
miRProf (miRNA Profiler): determines normalised expression levels of sRNAs matching known miRNAs in miRBase.
Hairpin Annotation: generates a secondary structure from an RNA sequence and highlights regions of interest using RNAplot
VisSR (Visualisation of sRNAs): generate a visual representation of sRNAs and user-imported genomic features.
PAREsnip2: Identify miRNA targets evidenced through the degradome

New Release
This version has two Java binaries. The first, ‘Workbench.jar’, is the standard binary for running the Workbench using the graphical user interface or through the command line. The second, ‘ServerWorkbench.jar’, is a version that can only run through the command line but does not require any JavaFX dependencies. This second version should hopefully resolve many problems regarding servers and machines that do not have the required libraries for JavaFX.

We highly recommend using the latest version of the Java 8.

This release contains the Alpha build for our latest workflow tool PAREsnip2, a much faster version of miRCat2, and a new version of FiRePat.
[ sRNA Workbench release history ]

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