Two sequences can agree at most positions and still leave us with a few awkward decisions. Is a leucine opposite an isoleucine a reasonable match? Should an alignment insert a gap here, or accept three mismatches and keep going? A scoring scheme puts numbers on those choices, and changing the numbers can change the alignment you get.

PAM and BLOSUM are families of substitution matrices for proteins . They describe how amino-acid pairs occur in aligned related sequences, relative to the pairs we would expect from their individual abundance. We will work through those counts, then use BioseqDB to calculate nucleotide and protein comparisons from 1,000 human mitochondrial genome records. SQL will do the counting and matrix calculations. Python will draw the results.

A protein is a chain of amino acids .…