So, I have a file with 600+ sequences of a gene, each one from a different population. This file was obtained after blasting the chromosome sequences against the gene sequence. However, I need the coding regions as well. Should I do the same and blast the chromosomes against the exons, or should I blast the gene sequences against the exons?
Not all the exonic sequence is coding. The ends have 3' and 5' UTRs.
Can you find gtfs for your organism? Those would be easier to work with.
Or, I'd do blastx against the protein, that should pull out just the sequence that codes for protein.