[ensembl-dev] biomart or perl API

Andrea Edwards edwardsa at cs.man.ac.uk
Sat Oct 23 13:18:41 BST 2010


I am new to ensembl and would like to perform some SNPs analysis. I 
don't know whether I should use the Ensembl variation API or whether to 
use BioMart. I've looked through the API tutorial and it seems to do all 
that I need which includes:

1) get all of the SNPs on a chromosome
2) get the alleles and db XREF for each SNP

Are there any particular reasons or advantages why I should use biomart 
over the Perl API.

Also are there any guidelines or restrictions if I want to perform any 
bulk processing on the ensembl server. As an example of bulk processing 
I mean getting summary info for all of the SNPs in an organism such as 
cow or mouse.

Many thanks

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