Reconstruct sequence based on conserved region

Question

[Human]

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!

[Michael]

If you have some sequencing reads, why don't you assemble them first into contigs and then check if your gene sequence can be aligned to the assembly?

[Human]

Basically I need a code to check if a sequence (a sex specific gene) is present in a huge pool seq fasta file, and see a portion of the neighboring sequences as well (left and right next to the sequence I searched for). What would you recommend?