How to bioinformatically locate information about genes (and corresponding proteins) given the gene name only?
2
1
Entering edit mode
9.5 years ago
cw00137 ▴ 10

I have a list of genes i.e.:

FOXG1
SNRNP70
CREBBP
JUN
FHL1
SNW1
FHL3
FHL2
...
...

My question is how can I use python or perl to automatically retrieve the corresponding accession numbers for the UniProt database? I'm looking for the name of the package and classes/methods as I'll be able to figure out the programming myself. I'm just having difficulties identifying the correct tools for the job.

Thanks

protein gene Perl Python API • 2.8k views
ADD COMMENT
6
Entering edit mode
9.5 years ago

You can use one of the APIs for biomart. Here's an example query, just click on the perl link for how to reproduce it with the perl API.

ADD COMMENT
1
Entering edit mode
9.5 years ago

Have a look at this page:

http://www.uniprot.org/help/gene_symbol_mapping

ADD COMMENT

Login before adding your answer.

Traffic: 2527 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6