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Extracting amino acid positions from a fasta sequence

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?

fasta

> abc 
atgcatgcgggcctttt
> cvb 
atgcatgcgggcctttt
> bnh 
atgCCcatgcgggcctttt

aligned

> abc 
atg--catgcgggcctttt
> cvb 
atg--catgcgggcctttt
> bnh 
atgCCcatgcgggcctttt
fasta python
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updated by rpolicastro rpolicastro • written by akang akang

Your question is not clear

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written by DareDevil DareDevil

I think, the position should be set according to the reference. Thank you.

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written by MSRS MSRS

Are you sure aligning before translating makes sense?

If you have insertions and substitutions, you should translate these first. If this leads to a frameshift for example, the result would be a radically different protein.

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written by Joe Joe

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