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Transmembrane helix prediction
For prediction of transmembrane helices, TMHMM version 2.0 [Krogh et al., 2001] is used. It is located at:
http://www.cbs.dtu.dk/services/TMHMM/
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 and in the original research paper [Krogh et al., 2001].
