I'm trying to reconstruct a gene sequence based on a PoolSeq file of a population (fasta format) and a conserved area. I want to search the file for matches with this sequence and then build up the neighboring area starting from that conserved sequence.
So I basically need a Bash command to search a fasta file for a sequence segment and to print the neighboring region of the match in every read.
File: Fasta file of dieverse Individuals of a species
Input: 20-30 bp Sequence
Output: All reads with that sequence and the neighboring region in that read
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