I have a list of gene of interest, a list with the position of coding sequences and a genome file (fasta from ncbi). While working with this non-model organism I was told that I need to trim away the sequence that code for a gene and retain the upstream sequence to look for TF binding sites. Is there any R package that does this trimming ? Or is this wrong? Some posts suggest using blastX, I know that it converts nt to protein sequence but I cannot figure out how it works, any help or any previous posts( that I missed) is appreciated, thank you.