Adding support for non-canonical amino acids #1
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And added final dictionary comma
Before, the script treated unrecognized residues as "" (null strings) in the sequence contstructed for alignment. This resulted in numbering mismatches for mutations after the non-canonical residue, and the wrong residue being centered and highlighted for disply. Now, the script treats all non-canonical sequences as "X" when aligning. Mismatches between non-canonicals are given a generic, BLOSUM-style score of -4 (e.g. "A"->"X"), and matches a score of 5.
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Before, the script treated unrecognized residues as "" (null strings) in the sequence constructed for alignment. This resulted in numbering mismatches for mutations after the non-canonical residue, and the wrong residue being centered and highlighted for display.
Now, the script treats all non-canonical sequences as "X" when aligning. Mismatches between non-canonicals are given a generic, BLOSUM-style score of -4 (e.g. "A"->"X"), and matches a score of 5.