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Approximate matching to find similar DNA sequence

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?

genome
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written by zhangdengwei zhangdengwei

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

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written by GouthamAtla GouthamAtla

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

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written by zhangdengwei zhangdengwei

2 answers

take a look here - fuzzysearch

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written by Assa Yeroslaviz Assa Yeroslaviz

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

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written by zhangdengwei zhangdengwei

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

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written by zhangdengwei 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.

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written by zhangdengwei zhangdengwei

or this agrep

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written by Assa Yeroslaviz Assa Yeroslaviz

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!!!

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written by zhangdengwei zhangdengwei

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