sRNA Workbench Version 2.2

sRNA Workbench Version 2.2: Released: 21/02/12

Includes improvements and bug fixes relating to several tools for all operating systems:

  • The hairpin annotation tool was colouring an extra nt for each short sequence highlighted on the secondary structure plot. This has now been addressed and fixed
  • miRCat “show in VisSR” now targets and zooms to the exact region on the chromosome
  • The search function was not performing correctly in the miRCat output table, it should now check all columns. Users are now also warned when the value searched for was not found
  • miRCat parameters have undergone a slight tweak for the plant default values (note, animal defaults have not changed for this version):
  1. Minimum hairpin length has changed from 150 to 60 after it was discovered that 150 would cause miRCat to miss many hairpins found in miRBase.
  2. Sequence Flank Extension length has been reduced to 100 as this proved to be a more effective default value.
  • SiLoCo is now available from the command line using the “–tool siloco” instruction. More information on executing Workbench tools from the command line can be found in the Quick-Start pages
  • MiRProf is now available from the command line using the “–tool mirprof” instruction. More information on executing Workbench tools from the command line can be found in the Quick-Start pages
  • Logging information is now output from all server threads and the main program giving users a record of any jobs they have ran through the workbench and information on why a job may have failed. Logs can be found in the user/logs directory

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