PRODIV-TMHMM is a hidden Markov model (HMM)-based service that does topology predictions for transmembrane proteins. In phylogenetics, "topology" is the pattern of branching in a phylogenetic tree, which shows the evolutionary relationships among groups of organisms. PRODIV-TMHMM accepts input in the form of a text file containing an amino acid sequence in FASTA format. The service then returns three-state topology predictions for each residue of the sequence. For increased accuracy, users may supply evolutionary information for the protein in the form of an alignment.
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