BLASTP (protein blast): Is the polar-nonpolar mismatch between amino acids scored differently than the polar-polar mismatch?

01 April 2021 1 5K Report

Which score should I focus on for that? Thank you!

The substitution matrices which blast uses to score alignments are based on the probability with which a given amino acid changes to another over large evolutionary distances, so there are different values for each pair of amino acids ( https://arep.med.harvard.edu/seqanal/matrices.html and literature cited therein)

They were derived by statistically analysing large numbers of aligned homologous sequences. For more details, see this book chapter: Chapter Substitution Matrices

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