Approximate matching to find similar DNA sequence

Question

[zhangdengwei]

Hi,

I am trying to fuzzily match a DNA sequence, like "ATCATTA" in "agATCGTTAgtatt", but I would like that some errors can be tolerant, such as mismatch, insertion or deletion for seed sequence - "ATCATTA". Do you have any method with Perl or Python?

[GouthamAtla]

The solution depends on how many such sequences you have and how many to search.

[zhangdengwei]

Wonderful !!! It works well. Lots of thanks to you!

Answer 1

[Assa Yeroslaviz]

take a look here - fuzzysearch

[zhangdengwei]

Wonderful !!! It works well. Lots of thanks to you!

[zhangdengwei]

Wonderful !!! It works well. Lots of thanks to you!

[zhangdengwei]

hi, I had a further question. I want to match the pattern "aggacctgct.+aggcgctcaacgg" for "aggacctgctGGCCAAGACCGCTGAGAACAaggcgctcaacgg" using fuzzysearch, but it couldn't work. And how can I take the subsequence out if there are some errors in the pattern? Thanks.

Answer 2

[Assa Yeroslaviz]

or this agrep

[zhangdengwei]

I could approximately match a subsequence by agrep, but if I would like to only take the subsequence out rather than the whole row, what should I do? And I haven't found the related parameters to address the problem. Thanks!!!