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Old 05-29-2015, 12:45 AM   #1
Location: New Jersey

Join Date: Sep 2012
Posts: 12
Question 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
mm.perrineau is offline   Reply With Quote
Old 05-29-2015, 05:25 AM   #2
Senior Member
Location: Ohio

Join Date: Jan 2010
Posts: 144

Maybe check out snpEff?
cliffbeall is offline   Reply With Quote

gff3, scaffolds, snp, synonymous

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