HMM-TM is a Hidden Markov Model method for the topology prediction of alpha-helical membrane proteins that incorporates experimentally derived topological information.
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BMC Bioinformatics. 2006 Apr 5;7:189.
Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins.
Bagos PG, Liakopoulos TD, Hamodrakas SJ.