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sRNAWorkbench

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The UEA sRNA Workbench

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Description

A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data

sRNAWorkbench Web Site

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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Additional Project Details

Intended Audience

Science/Research

User Interface

Java Swing

Programming Language

C++, Java

Registered

2012-01-25

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