from genome position to protein position

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3.3 years ago

vujex ▴ 10

Hello,

Does anyone know a tool to go from genomic positions to protein and to see whether SNPs are (non)synonymous in bacteria?

Doing it manually in IGV would take too much time...

I have experience with Python, R and bash.

Thanks in advance,

protein snp genome bacteria position • 1.4k views

ADD COMMENT • link 3.3 years ago by vujex ▴ 10

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Convert SNPs into text file that VEP can accept (or VCF) and assuming that mentioned bacterial genomes are sequenced and annotated, VEP will furnish syn, non-syn annotations of input SNPs

ADD REPLY • link 3.3 years ago by cpad0112 21k

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Thanks, the problem is that my bacterial genome is not on ensembl - I don't see a way to use VEP with a new genome...

ADD REPLY • link 3.3 years ago by vujex ▴ 10

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is it annotated?

ADD REPLY • link 3.3 years ago by cpad0112 21k

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it is annotated

ADD REPLY • link 3.3 years ago by vujex ▴ 10

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can you share the link for downloading annotated file?

ADD REPLY • link 3.3 years ago by cpad0112 21k

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It is this one H37Rv reference genome of Mtb: https://www.ncbi.nlm.nih.gov/assembly/GCF_000195955.2 For some reason it seems to have disappeared from ensembl....

ADD REPLY • link 3.3 years ago by vujex ▴ 10

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