How to find a specific sequence pattern in a fasta file?
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
I have a fasta file as follows,
gene.fasta
The expected output should be like this,
In order to mine the above mentioned pattern, I have used grep command but, I do not know how to specify only 3 bases for Z and also I could not specify N16 criteria in the grep command line. In addition to this, I do not know how to mine the 5 of the flanking bases along with the pattern. So kindly help me in this regard.
Thank you in advance.
Last edited by dineshkumarsrk; 11-29-2019 at 07:15 AM..
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