Ensembl biomart attribute for number of synonymous vs. non-synonymou sites
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5.5 years ago
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I am trying to obtain the number of synonymous and non-synonymous sites for a gene. I know that ensembl provides attributes like "mmusculus_homolog_dn" and "mmusculus_homolog_ds", i.e. the dn and ds values for a gene given mouse outgroup comparison, where dn = #non-synonymous mutations/#non-synonymous sites, and ds = #synonymous mutations/#synonymous sites. I need the denominators of these terms, i.e. the number of synonymous/non-synonymous sites in a gene (i.e. the number of possible silent and non-silent mutations per site summed over all sites in the cds). I searched the attribues page for biomart and nothing obvious came up with those terms, but I assume that this information is there with some attribute name that I couldn't identify.

Alternatively, if this information is not available from ensembl, is there another database that would have it?

Thank you.

ensembl biomart • 2.1k views
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5.5 years ago

I'm afraid that number is not accessible in BioMart, but you can get it via the Perl API.

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OK, thanks. Perhaps in the future this would be a useful attribute to add to the data base.

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