How To Retrieve Gene Family Alignment Data From Ensembl Database
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9.9 years ago
Jianguo Lu ▴ 200

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!

gene ensembl • 3.2k views
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Your question is very ambiguous. Please try to more specific so that we can help.

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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

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

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

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Thank you so much.

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9.9 years ago

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

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