The plugin uses TMHMM version 2.0, located at: http://www.cbs.dtu.dk/services/TMHMM/. Thus an active Internet connection is required to run the transmembrane helix prediction. The predicted helices can automatically be added to the sequence as annotation or predictions can be viewed in text.
When the plugin is installed, you will see an icon in the Toolbox under Protein Analyses.
Note! The plugin is available for CLC Main Workbench only.
For prediction of transmembrane helices, TMHMM version 2.0 is used. It is located at: http://www.cbs.dtu.dk/services/TMHMM/.
To predict transmembrane helixes, simply select the sequences of interest and run the analysis.
The predictions obtained can either be shown as annotations on the sequence or be shown as the detailed text output from the TMHMM method. After running the prediction as described above, the protein sequence will show predicted transmembrane helices as annotations on the original sequence.
Moreover, the annotations showing the topology will be shown. That is, which parts of the proteins are located on the inside or on the outside.
Each annotation will carry a tool-tip note saying that the corresponding annotation is predicted with TMHMM version 2.0. Additional notes can be added manually through the Add annotation right-click mouse menu. Undesired annotations can be removed through the Edit annotation right-click mouse menu.
Additional information on THMHH and Center for Biological Sequence analysis (CBS) can be found at http://www.cbs.dtu.dk.