Ensembl biomart attribute for number of synonymous vs. non-synonymou sites
1
0
Entering edit mode
9.1 years ago
Max ▴ 150

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 • 3.1k views
ADD COMMENT
0
Entering edit mode
9.1 years ago
Emily 24k

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1946 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6