Alignment with deletion

Question

[Guy]

Hello,

I have a DNA sequence with some deletions. I have a reference sequence, with deletions as well.

I want to align these reads pairwise. However, when I'm using Align packages (or others), it considers the deletions as mismatches:

Is there a method to count deletions as matches if performed in both sequences?

Thank you!

[GenoMax]

I want to align these reads pairwise.

How will the information be carried over if you are doing pairwise alignments? e.g. how would the aligner know to put a gap in the sequences if it is simply aligning the two sequences you show in the example above.

Answer 1

[Jeremy]

You can use EMBOSS Needle for DNA:

EMBOSS Needle

[Guy]

Thank you. Do you familiar with python package that I can integrate into a pipeline?