I work with a pretty uncharacterized bacterium (genome size 4Mb) and I have a collection of SNPs in my mutants. I would like to determine whether or not they are in coding regions and whether they impact the protein sequence.
At the moment I am using Galaxy for my analysis and I have an annotated genome of my bug and a list of SNPs (basepair, parent base call, mutant base call). Is there a way to determine for each SNP whether it is in a coding region and what impact the SNP has on the protein sequence (silent, missense, nonsense) besides looking at each by hand?
I'm pretty new to sequencing and bioinformatics, so appreciate all the help you can give me.
Thank you!
At the moment I am using Galaxy for my analysis and I have an annotated genome of my bug and a list of SNPs (basepair, parent base call, mutant base call). Is there a way to determine for each SNP whether it is in a coding region and what impact the SNP has on the protein sequence (silent, missense, nonsense) besides looking at each by hand?
I'm pretty new to sequencing and bioinformatics, so appreciate all the help you can give me.
Thank you!
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