When the plugin is downloaded and installed, you can use it to predict transmembrane helices:
Toolbox | Classical Sequence Analysis () | Protein Analysis () | Transmembrane Helix Prediction ()
If a sequence was selected before choosing the Toolbox action, this sequence is now listed in the Selected Elements window of the dialog. Use the arrows to add or remove sequences or sequence lists from the selected elements.
The predictions obtained can either be shown as annotations on the sequence, in a table or as the detailed and text output from the TMHMM method.
- Add annotations to sequence
- Create table
Click Next if you wish to adjust how to handle the results, then click Finish.
You can perform the analysis on several protein sequences at a time. This will add annotations to all the sequences and open a view for each sequence if a transmembrane helix is found. If a transmembrane helix is not found a dialog box will be presented.
After running the prediction as described above, the protein sequence will show predicted transmembrane helices as annotations on the original sequence (see figure 1.5). Moreover, annotations showing the topology will be shown, i.e., which part the proteins is located on the inside or on the outside.
Each annotation will carry a tooltip note saying that the corresponding annotation is predicted with TMHMM version 2.0. Additional notes can be added through the Edit annotation () right-click mouse menu. Undesired annotations can be removed through the Delete Annotation () right-click mouse menu.