I am trying to align two sequences. I have the error information for the insertion/deletion of each letter(A,G,T,C). How do I effectively incorporate this into the gap penalty?
alignments = pairwise2.align.globalms(X, Y, 1, -1, -1, -0.1, force_generic=True)
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trinityduke100 •
You can specify a dict of lists that define nucleotide substitution scores. See this answer for an example:
Custom substitution matrix in biopython pairwise2 aligner
Note you need to specify this the d option. Read the documentation:
https://biopython.org/docs/1.75/api/Bio.pairwise2.html
I believe the function call would be:
pairwise2.align.globalds(X, Y, match_dict, ...)
Yes but is this for substitutions(mismatch) errors?
I have a particular sequence that is passed through a channel which results in insertion, deletion and substitution errors.
I have these probabilities but all insertions and deletions appear as gaps in the alignments.
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