COMA (Comparison Of Multiple Alignments) is a method for detection of distant evolutionary relationship (homology) through comparison of multiple protein sequence alignments. For convenience, the COMA software package includes programs for constructing profiles from multiple alignments, generating a profile database from a set of profiles, searching a profile (multiple alignment) against a profile database, etc. COMA output consists of pairwise alignments between profiles (multiple alignments) with estimated values of statistical significance, which indicates the probability that the aligned pair of profiles is a random match.
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Margelevičius M., Venclovas Č. (2010)
Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparisons.
BMC Bioinformatics, 2010 11:89.