TMpred - Prediction of Transmembrane Regions and Orientation

The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring. 
K. Hofmann and W. Stoffel
TMbase - A database of membrane spanning proteins segments
Biol. Chem. Hoppe-Seyler 347,166 (1993)

For further information see the TMbase and TMpredict documentation.

Choose the minimal and maximal length of the hydrophic part of the transmembrane helix

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