The UEA Small RNA Workbench Suite of tools for analyzing small RNA data from Next Generation Sequencing devices
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The UEA Small RNA Workbench Description

The UEA Small RNA Workbench is an application developed to help biologists analyze single or multiple-sample sRNA data from plants and animals. You can use this application to identify interesting landmarks (such as detection of novel micro RNA sequences) or other tasks such as profiling small RNA expression patterns in genetic data. Main 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. miRCat (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. PAREsnip: Identify miRNA targets evidenced through the degradome

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