HomeCLC software: Important notificationsIssues affecting only versions of products released prior to June 2017SignalP and TMHMM plugins not working in older Workbenches (7.0 and earlier)

3.14. SignalP and TMHMM plugins not working in older Workbenches (7.0 and earlier)

Working versions of the TMHMM and SignalP plugins have been released for:

  • Genomics Workbench versions 7.0.3 as well as point versions 7.0.1 and 7.0.2
  • Main Workbench version 7.0.2 as well as point version 7.0.1
  • Drug Discovery Workbench 1.0.2 as well as point version 1.0.1

This fixes the problem described below.

Please note that the plugins in older versions of the Workbench are still currently affected.  (Entry date: May 2014).

If you are using one of the versions of the Workbenches listed above and you have one or both of these plugins installed, you should see a pop-up box inviting you to update them if they are not the latest version. You will need to be running the Workbench as an administrative user to update plugins.

If you are running an older version of a Workbench, and your license is currently covered by our Maintenance, Upgrades and Support (MUS) program, then we recommend that you upgrade to the latest version of the Workbench. If you are connecting to a Server product from your Workbench, then please make sure that your Server is in the 6.x line before carrying out this upgrade.

 

Who do the SignalP and TMHMM problems affect?

This issue affects signal peptide prediction using the Signal P plugin and TMHMM analysis using the TMHMM plugin in the Main, Genomics and Drug Discovery Workbenches older than those listed at the top of this page.

Symptom

  • In the Main and Genomics Workbenches version 7.0, the analyses fail with a java null pointer exception.
  • In earlier versions of the Workbenches, the results of SignalP analysis suggest that no signals have been detected, but in fact, the analysis has not run properly.

The underlying issue

For prediction of signal peptides and transmembrane helices, the Workbench uses SignalP and TMHMM, respectively, as made available as a free service from a third party. Unfortunately the services used in these plugins, which are not identical to the public SignalP and TMHMM webservices, are currently not responding.

We continue to hope that the third party providers will make these services available again in the future, but we do not have control over this.

 

Suggested Workarounds for people using older Workbenches

Signal P workaround

The public SignalP webservice appears to still be available. To run your analysis you can submit your input data manually to that webservice. To do this:

  1. Use the mouse to select the input sequence and copy it using ctrl+C/cmd+C. Alternatively, export the sequence(s) in FASTA format.
  2. Go to the webservice http://www.cbs.dtu.dk/services/SignalP/.
  3. Paste the sequence into the webservice or use the generated FASTA file as input.
  4. Set the parameters as appropriate and press 'Submit'.
  5. The calculation will start. Specify an email address and press 'Send email' to get the calculation to return the results.


Transmembrane Helix Prediction workarounds

a) Use the public webservice by manually transferring the input data

  1. Use the mouse to select the input sequence and copy it using ctrl+C/cmd+C. Alternatively, export the sequence(s) in FASTA format.
  2. Go to the webservice http://www.cbs.dtu.dk/services/TMHMM/
  3. Paste the sequence into the webservice or use the generated FASTA file as input.
  4. Press 'Submit'
  5. The calculation will start. Specify an email address and press 'Send email' to get the calculation to return the results.
  6. The range of residues predicted to be in transmembrane helices (TMhelix) are specified in the results.

b) Use the hydrophobicity scales provided with the workbench:

  1. Open the sequence of interest and go to the 'Protein info' tab in the side panel.
  2. A variety of hydrophobicity scales are listed. Choose e.g. Kyte-Doolittle
  3. Apply it as background color. Segments of hydrophobic residues will then show up in red. Hydrophobic segments of length around 20 residues and with an alpha-helix secondary structure will indicate the potential transmembrane helices.

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