It sounds like something that should be straightforward, but probably nobody here knows what a FASTA file is. If you can post a sample of the input and a sample of the expected output, that would help a lot. Posting some code that you've started with would help even more-- there have been a bunch of bioinformatics problems with responses posted over the past few days that you could probably use as a starting point

In reply to Re: inexact PAttern searching by bitingduck
in thread inexact PAttern searching by Chauds09

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