I need a suggestion regarding extracting positions from a nucleotide fasta file.
I have a fasta file like below. I am aligning the file ,then converting the sequences into amino acid sequence and finally extracting specific amino acids (say position 1,3,4) from the amino acid data. But since their is an insertion in one sequences it messes up the positions in others. So when I say aa at position 2 for abc is X, cvb is X and bnh is T. will that be correct?
> abc atgcatgcgggcctttt > cvb atgcatgcgggcctttt > bnh atgCCcatgcgggcctttt
> abc atg--catgcgggcctttt > cvb atg--catgcgggcctttt > bnh atgCCcatgcgggcctttt