Bipartite scoring scheme. Bipartite scoring scheme for the detection of homologous transmembrane proteins from Ref. . The figure represents the Smith-Waterman alignment matrix and indicates which scoring matrix is used for which query positions (rows): In transmembrane helices, a transmembrane-specific scoring matrix is used. For p-value computations, the query is assumed fixed or generated by the TMHMM and the subject is assumed a random i.i.d. sequence drawn from the distribution of amino-acid frequencies of the database.