Best pairwise alignment for insertion and deletion-containing sequences

Question

[rbpdee]

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":

Answer 1

[patrickdm]

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.

[rbpdee]

Thanks, patrickdm! Let me give it a shot.