Transmembrane Helix Prediction (DeepTMHMM)
For prediction of transmembrane helices, this tool uses DeepTMHMM [Hallgren et al., 2022] located at https://dtu.biolib.com/DeepTMHMM, thus an active internet connection is required to run the transmembrane helix prediction. Additional information on DeepTHMHH can be found at https://dtu.biolib.com/DeepTMHMM and in the original research paper [Hallgren et al., 2022].
When the plugin is downloaded and installed, you can use it to predict transmembrane helices:
Toolbox | Classical Sequence Analysis (
) | Protein Analysis (
) |
Transmembrane Helix Prediction (DeepTMHMM) (
)
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 a protein sequence or protein sequence list.
The predictions are shown as annotations added to the input sequence or sequence list.
After running the prediction as described above, the protein sequence will show predicted transmembrane helices as annotations on the original sequence (see figure 3.2). Moreover, annotations showing the topology will be shown, i.e., which part the proteins is located on the inside or on the outside.
Figure 3.2: Transmembrane segments shown as annotation on the sequence and the topology.
Each annotation will carry a tooltip note saying that the
corresponding annotation is predicted with DeepTMHMM.
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.