Can I programatically query Ensembl's blast servers?

Question

[dchen71]

I am trying to find where probes lie on mice genome. I have tried using blat locally and have gotten about 40% located which appears to fall in line with checking the first 100 probes via UCSC. Using Ensembl's blast, I found that I could find hits for every probe but the issue being that I have >1000 probes to check.

Is there a programmatic way to query ensembl for this data?

[Emily]

Are the probes from a commercially available microarray? If so, which one? We have mapping for many of these available in Ensembl, to both loci and genes.

[dchen71]

Thanks for everyone's posts, they were all helpful. I ended up going with a local blast database as it seemed like the best alternative.

Answer 1

[Jean-Karim Heriche]

You can download Ensembl data from their ftp site then build a local blast database.

Answer 2

[LLTommy]

Besides the post above, Ensembl offers APIs for access via programming. You can find the Perl API here and the REST API here.

[Emily]

Neither can be used for BLAST though.