Sequence tools

DNA: standard genetic code (NCBI table 1); an ORF runs from ATG to the first in-frame stop codon on both strands. Melting temperature by the Wallace rule below 14 bp and by the GC formula above. Protein: average residue masses minus one water per peptide bond; pI by bisection with Bjellqvist-type pK values; extinction coefficient = 5500·W + 1490·Y, plus 125 per cystine pair; Kyte-Doolittle hydropathy. Protein values match Biopython. The protein example is human insulin, UniProt P01308. Alignment: Linear gap penalty; end gaps are penalised in global mode. Ties in the traceback prefer the diagonal. The protein pair is the classic example from Durbin et al., Biological Sequence Analysis, which scores it with BLOSUM50, so the book's numbers differ. Scores match Biopython's PairwiseAligner.