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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