This namespace contains constants for selecting protein sequence alignment distance matrices.
Do not use a protein alignment distance matrix.
Use an identity matrix for protein alignment distance calculation (+1 if residue type is identical, otherwise 0).
Use the PAM250 protein alignment distance matrix [Dayhoff-1978]. This matrix uses weights derived from an estimate of evolutionary substitution rates from a database of 71 groups of closely related, mostly globular proteins, with an evolutionary distance of 250 substitutions per hundred residues. This matrix is is best used when aligning similar proteins.
Use the Blosum62 protein alignment distance matrix [Henikoff-1992]. This matrix uses weights derived from alignable regions from the BLOCS database for distantly related proteins.
Use the Gonnet protein alignment distance matrix [Gonnet-1992]. This matrix uses weights derived from exhaustive pairwise alignments of the protein sequence databases. This matrix is useful for alignments proteins of varying similarity.