Reconstruct sequence based on conserved region
I am searching for a smart way to reconstruct a sequence next to a gene of interest to set primers. For this I want to use the sequence of a gene from NCBI, search for it in my raw fasta files, and in case of a perfect match, get a part of the neighboring sequences as well.
So far I'm using this one liner:
perl -lane ' if ($_ =~ "sequence xy") {@array=split("right part of sequence xy"); print $array[1]}
But like this I don't know when the gene actually ends and also I don't know how to go "to the left side".
Maybe there is a smarter solution to do it with one command only.
Thanks in advance!
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