[ensembl-dev] MySQL query to retrieve protein annotation

[Charles Joseph Murphy]

Thanks for your suggestion.

Sorry to bother with another question, but I’ve spent a couple hours trying to figure this out and wonder if either of you could help me with something else. How might I go about getting the descriptions of the protein annotations. For example, for PFAM domains I want what is displayed on the Ensembl website. E.g. “Pkinase” instead of PF00069.

Thanks!

On Feb 23, 2017, at 04:30, Michal Dabrowski <m.dabrowski at nencki.gov.pl<mailto:m.dabrowski at nencki.gov.pl>> wrote:

How about removing the table "translation" in the FROM part of your query?
Or adding sth like " AND translation.translation_id='291089’ " to the WHERE part.
Now it seems you will get all the entries from the "translation" table.
m.

Michal Dabrowski
Laboratory of Bioinformatics
Nencki Institute
Pasteur 3 Str
02-093 Warsaw, Poland
phone: 48 22 58 92 575


On Feb 22, 2017, at 5:43 PM, Charles Joseph Murphy wrote:

Hi,

I’ am trying to use the Ensembl public MySQL query to retrieve protein annotation for all of a genome’s genes. While trying to figure out the right MySQL queries to make, I’ am testing it out with just one transcript’s translation (ENSMUST00000120187):

mysql> use mus_musculus_core_75_38;
mysql> SELECT protein_feature.hit_name, protein_feature.hit_start, protein_feature.hit_end, protein_feature.seq_start, protein_feature.seq_end, protein_feature.evalue, protein_feature.perc_ident, protein_feature.hit_description, protein_feature.translation_id FROM protein_feature, translation WHERE protein_feature.translation_id = '291089’;

But this returns around 1.4 million entries. What might be the best way to get all the protein annotation for ENSMUST00000120187? I’ am aware of BioMart and the Perl API, but would rather query via MySQL. I’ am continuing to read into the InterProScan pipeline and Ensembl documentation, but am not quite sure yet how to go about this.

Thanks for any help!
Charlie
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