How To Retrieve Gene Family Alignment Data From Ensembl Database

Question

[Jianguo Lu]

How to retrieve gene family data (alignment data is better) in Ensembl database? I just want to get fish species whole genome-wide gene family data. Appreciate it!

[Davy]

Your question is very ambiguous. Please try to more specific so that we can help.

[Vitis]

it works just like any API, you have to program a little bit to get things. In general, it looks like a perl interface to mysql databases (so if you know perl DBI, it works just like that). Here is the tutorial: http://useast.ensembl.org/info/docs/api/compara/compara_tutorial.html

[Vitis]

I think ensembl compara has an API but I never used it before. That might be what you want.

[Jianguo Lu]

Yes. I know API can do this job. But I don't know how to use API.

[Jianguo Lu]

Thank you so much.

Answer 1

[Javier Herrero]

Hi Jianguo

If you prefer to flat files, we also provide EMF dumps in Ensembl: ftp://ftp.ensembl.org/pub/release-66/emf/ensembl-compara/homologies/

EMF is a column-based multiple alignment format. Read more on this at: ftp://ftp.ensembl.org/pub/release-66/emf/ensembl-compara/epo_6_primate/README.emf