Entering edit mode
2.0 years ago
Guy
▴
10
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!
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.