sRNA Workbench Version 2.3.2 Released

The sRNA Workbench is a Java based suite of tools for analyzing small RNA/miRNA data from Next Generation Sequencing devices. Latest version is 2.3.2 and was released yesterday.
The update covers several bug fixes and behavior modifications relating to all operating systems and several tools.

sRNA Workbench home page:
http://srna-workbench.cmp.uea.ac.uk/

Direct download link:
http://sourceforge.net/projects/srnaworkbench/

Changes and fixes in detail:

Adapter Removal

• Adapter removal was inaccessible from the command line. This issue has now been resolved

miRCat:

• miRCat was inaccessible from the command line. This issue has now been resolved
• miRCat had an issue when creating large amounts of RNA annotation renders (when outputting to disk) potentially causing some entries in the legend to be missed. This has now been resolved
• miRCat should now correctly output GFF records that can be read by any genome browser
• When running miRCat from the command line, the mature miRNA sequences are now written to a file called miRNA.fa and stored in the output directory
• When running miRCat from the command line a user no longer needs to have updated miRBase from the GUI first (however, if no miRBase files are detected then the tool will not be able to look for known miRNA sequences)

RNA annotation

• RNA annotation was incorrectly colouring extra nt when the short sequences were overlapping the ends of the long sequences. This affected both the GUI and when activating the tool directly from miRCat, this should now work correctly
• When rendering large amounts of hairpins to disk the hairpin tool would not show the hairpins (leaving them in the selected directory). This behaviour has been modified, the RNA annotation tool now has the ability to navigate directories of hairpin images including those generated by miRCat when rendering large amounts of results
• Any RNA Annotation frames generated from miRCat when in file mode (i.e. when rendering large amounts of results) are locked to that specific directory and cannot have new hairpins added to them, however, new RNA annotation frames can be created in the usual way
•     A new window showing progress of RNA annotation renders from miRCat has been added
•     When rendering RNA plots directly from miRCat the colours of the highlighted regions (miRNA and miRNA*) should now match the highlighted text in the miRCat output table (blue for miRNA and red for miRNA*)
• Rendering large amounts of hairpins has now been moved to a separate thread to prevent locking the main workbench thread
• Hiding the sequence options in the tool will now also hide the colour palette
• The labels in the colour chooser now change their colour to reflect the selected colour for the respective short sequence

General:

• Changed logging level of certain messages from miRCat and RNA annotation to stop the printouts appearing in the console window when they are not needed
• The menu system from the main window has been slightly overhauled to match the menu system on the website and in preparation for new tools coming soon