Download Ensembl Blastn Result

Question

[Nicolas Rosewick]

Hi,

How can I download blast results from ensembl. I blast 10 sequences against all ensembl species. Now I have the result page and I want to download all hits to compare them.Is it possible ?

Here's the result page : http://www.ensembl.org/Multi/blastview/BLA_e7BED9oDE

Thanks,

N.

Answer 1

[Manu Prestat]

It's easy to retrieve them, just click on the [RawResult] links. I anticipate the next issue, what to do with that flat blast output format? What do you want to compare? It is sometimes easier to work with an XML or a tabular format. In case you want to convert those in a table (-m 8 style), you might find this script interesting. However, the spaces in the subject names could be an issue. You could try to "sed" these before, for instance:

sed '/>[0-9]*/ s= =_=g' res.blast