Download Gene Trees and Sequences from ensembl

Question

[ddowlin]

Hi,

I have a list of human ensembl gene ids. I want to download gene trees and corresponding sequences from ensembl so that I can calculate Dn/Ds ratios.

So far I have been able to get this information by manually searching ensembl, clicking gene trees, then selecting my clade, and downloading the trees and sequences.

As I have a large list of genes doing this by hand would be both tedious and time consuming.

Is there a way to automate this process? So that I could provide a list of gene ids and the clade of interest.

Many thanks.

Answer 1

[Denise CS]

Ensembl may have already calculated Dn/Ds ratios. You can retrieve those either with BioMart (through a web interface or in R with biomaRt) or with the Perl API. Check the Compara API tutorial.

[Denise CS]

p.s. Ensembl calculates dN/dS values between closely-related species only. You can download the tree and the sequences as shown by Matthieu Muffato Workshop materials.

[ddowlin]

Thank you. I had already tried some of my genes using biomart and the dN/dS were missing. I will take a look at the materials you provided.