Protein ID and Protein domain ID description
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6.9 years ago
Lalla ▴ 40

Hi!

Given a list of protein IDs how can I retrieve the description and information (for example protein domains) related to them in a systematic way?

Specifically I'd like to know how 2 different proteins from a same gene differ in their domains, structure and function.

Is there a database I can query for that?

I would also like to know where can I find the description of protein domains of different type (PFAM, Interpro, etc), without query every single Id in each database.

 

Thanks

protein protein domain • 3.4k views
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6.9 years ago
venu 7.0k

PDBe REST API. Many options are available. Just explore it.

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6.9 years ago
Lalla ▴ 40

Thanks a lot!

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6.9 years ago

Have you tried UniProt? Documentation on how to access uniprot.org programmatically can be found here: http://www.uniprot.org/help/programmatic_access

You could submit a list of UniProt identifiers in the form "accession:P12345 or accession:P99999 or accession:P04406" and then use the "Columns" button to customize your output, e.g. to add columns for InterPro, Pfam etc domains.

http://www.uniprot.org/uniprot/?query=accession:P12345 or accession:P99999 or accession:P04406&sort=score&columns=id,entry name,genes,length,comment(DOMAIN),feature(DOMAIN EXTENT),database(InterPro),database(Pfam),database(PROSITE)

This URL can be used programmatically, in particular to download the same information in tab-delimited format:

http://www.uniprot.org/uniprot/?query=accession:P12345%20or%20accession:P99999%20or%20accession:P04406&format=tab&columns=id,entry%20name,genes,length,comment(DOMAIN),feature(DOMAIN%20EXTENT),database(InterPro),database(Pfam),database(PROSITE)

 

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6.9 years ago
Lalla ▴ 40

Thanks, but I have to do the opposite, I have a list of different domain Ids from different databases and I would like to find their description without enter each single ID (or group of IDs of a same type) into the respective database.

Those IDs are a results of a Perl Ensembl API query, maybe there is a way to add the description as an output of that directly in the perl code? It still seems odd that there isn't an easy way to get the descriptions from the IDs. I tried alsowith biomaRt but it seems it doesn't allow to select multiple filters for the protein IDs.

@venu, I had a look at the PDBe REST API but it doesn't seem that it does what I need
 

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