Alignment with deletion
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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: enter image description here

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

Thank you!

match deletion alignment • 857 views
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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.

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2.0 years ago
Jeremy ▴ 930

You can use EMBOSS Needle for DNA:

EMBOSS Needle

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

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