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  • How to know if a SNP is non synonymous using the genome sequence and the gff3 file?

    Hi everyone,
    Everything is in the title: How to know if a SNP is non synonymous using the genome sequence and the gff3 file?
    I have no other information than the SNP position in the genome, the scaffolds in fasta format and the gff3 file.
    In the past, I check manually few mutations ie:
    1) I extract few nt around the SNP
    2) I modified manually the sequence
    3) I translate both sequences (originel and modified) in the good frame
    4) I align both
    But know I have to do that for more.
    I anybody can help me?
    Thank you very much

  • #2
    Maybe check out snpEff?

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