Entering edit mode
3.8 years ago
trinityduke100
▴
10
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)
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.
You can define a callback gap function for such cases then:
Everything is in the documentation.