Best pairwise alignment for insertion and deletion-containing sequences
Hi folks,
What is the most accurate Biopython function for performing pairwise alignment of a 200-bp sequence against its reference? Some of my sequences may contain insertions and deletions, so handling indels accurately is important. I’d appreciate any suggestions or recommendations.
For example for a mutant read with insertion and deletions, I am interested in getting "Expected alignment" instead of "Alignment 1":
1 answer
Hello, I'd try tweaking the Affine Gap Scores of Align.PairwiseAligner(), and if those are not good enough, consider the possibilty to specify your own gap scoring function.
Hth.
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