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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
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
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