Question: Get the Protein-Accession - GO-ids mapping for every Protein in e.coli K12
0
gravatar for Benni
2.5 years ago by
Benni30
Benni30 wrote:

I only found the annotation file for e.coli from EcoCyc: "gene_association.ecocyc" But I can´t open the file. I just need a simple text file, that maps ProteinAccession to all GO-ids.

SOLVED: I just renamed the file to .gaf since it already is in the .gaf format.

go protein gene ontology • 949 views
ADD COMMENTlink modified 2.5 years ago by Elisabeth Gasteiger1.6k • written 2.5 years ago by Benni30
0
gravatar for Elisabeth Gasteiger
2.5 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

Glad you managed to get your data. Alternatively, you could also query UniProtKB, e.g.

http://www.uniprot.org/uniprot/?query=organism:83333 http://www.uniprot.org/uniprot/?query=proteome:UP000000625

and then customize your output to include a column for GO identifers, optionally remove all other columns, and download the file in tab-separated format (http://www.uniprot.org/help/customize)

This results in (preview of first 10 entries in the list): http://www.uniprot.org/uniprot/?sort=score&desc=&compress=no&query=organism:%22Escherichia%20coli%20%28strain%20K12%29%20[83333]%22&fil=&limit=10&force=no&preview=true&format=tab&columns=id,go-id

ADD COMMENTlink written 2.5 years ago by Elisabeth Gasteiger1.6k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1694 users visited in the last hour