Downloading All Gene Families From Mammalian Species In Ensembl

Question

[Marki]

Hello everyone,

Can anybody kindly guide me on what might be a simple and efficient way to download all gene families from mammalian species in Ensembl? I browsed through the online resources and they say that there may be more than one way to download data but I couldn't "shape" the query either on Ensembl or Biomart (don't know how mysql tool will work).

My apologies if this question seems too simple but I haven't used any of the biological databases before in such capacity.

Thanks in advance :) Marki

[Biojl]

I'm confused. In the title you ask for all gene families from mammalian genomes and in the question you ask to download all the mammalian gene families... Those are different things.

[Marki]

I have edited the question to make it more clear. I want to redo some analysis described in http://genome.cshlp.org/content/23/2/323.long (Results section)

Thanks for pointing out the mistake.

Answer 1

[Emily]

You can fetch gene families using the Compara API. There's a section on gene families in our online API course. If you're new to the API, you should look at the Core module before embarking on the Compara trees.