PRODIV-TMHMM is a hidden Markov model based server for topology prediction of transmembrane proteins. Details of the program can be found in: "Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information"; H嫡n Viklund and Arne Elofsson; Protein Science Vol. Protein Sci. 2004 Jul;13(7):1908-17; PRODIV-TMHMM provides three-state topology predictions for each residue of the sequence: membrane (M), inside (i) and outside (o). Input is a text file in FASTA format containing an amino acid sequence. For increased accuracy, evolutionary information about the protein in the form of an alignment may be supplied. This is done by putting the alignment sequences in the same FASTA file as separate FASTA format entries in the original query file. '-' signs are accepted as placeholder character in the alignments. FASTA file with query sequence and alignments. Each alignment should be given as an individual FASTA entry after the query. Gaps are represented by '-' (hyphen) characters. Text file (string) with PRODIV-TMHMM output. FASTA file with query sequence and alignments. Each alignment should be given as an individual FASTA entry after the query. Gaps are represented by '-' (hyphen) characters. Boolean indicating whether output should contain labelling of amino acids. Boolean indicating whether output should contain alignment information. Scoring method for alignment and profile data. Possible values are: DP,DPPI,GM,GMR,PI,PIS. Default is GM. Specify which columns to use for alignment input data. May be 'all' or a number, the number specifying a sequence in the alignment whose columns with non-gap symbols will be used. Default is 'all'. Text file (string) with PRODIV-TMHMM output. Run PRODIV-TMHMM with default parameters.

Run PRODIV-TMHMM with user defined parameters.