The UEA Small RNA Workbench – Version 2.4.2 Update

by Christoph on August 15, 2012

in Software

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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