There is an extensive API for the ensembl data, but it's a bit of a learning curve.

Perhaps this is an easier way to get at their sixway primate alignment: 

  Main site  http://www.ensembl.org/index.html 
-> links to  http://www.ensembl.org/downloads.html
-> links to  http://www.ensembl.org/info/data/ftp/index.html

There, the EMF link leads to:

ftp://ftp.ensembl.org/pub/release-66/emf/ensembl-compara/epo_6_primate
+/

(chromosome 11 is there, too)

[download]

The emf format is explained in a readme in that directory.

(if you prefer to get your stuff via the urls, make sure you give ample waiting times between the retrievals (i.e.: sleep 20, or whatever duration ensembl requests: it will be in their API's documentation ) or you risk being banned from ensembl servers.)

(BTW, it's EnsEMBL, without the -e. See EMBL)

In reply to Re: i need help to download text data from ensemble for a project by erix
in thread i need help to download text data from ensemble for a project by aaabc

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