1
$\begingroup$

I want to map some gene ids to their proteins structures if they exist. The genes are rows of this CSV. There are other information that may help also such as Product description but that may lead to anbiguities. I am looking for a programmatic way, biopython or pdb API?

$\endgroup$
  • 1
    $\begingroup$ From EMBL SIFTS you can download a table that goes from Uniprot ID to PDB and chain and numbers that can give you any offset. Do note that offset correction is a problem for about 10% —I use python's pymol2 module to fix these (yup, silly but best option). Also if the organism is common you might wanna check out SwissModel's premade threaded models of close homologues(20% id min) $\endgroup$ – Matteo Ferla Apr 30 at 12:54
2
$\begingroup$

Not sure if you want the structure exactly or a handle of some sort, but the best way i know to get ALL your 5000 identifiers to map to uniprot/pdb is uniprot's mapping service. You can either copy your ids straight from excel or parse with python ex.:

import pandas as pd
import os

file_name = 'aap7847_Zhang_SM_Table-S5.xlsx'
sheetname = 'Table S5'
df = pd.read_excel(file_name, sheet_name=sheetname, skiprows=1)
ids = list(df['Gene_ID'])

name_of_file_to_save_to = "geneIds.txt"
with open(name_of_file_to_save_to, "w") as newf:
    for id in ids:
        print("{}\n".format(id), file=newf)
    newf.close()

You can then save the Uniprot's response and either add it as a column to your file or map to other parts of Elixir ecosystem with SIFTS, for example, as @Matteo Ferla says. enter image description here


In the case that you maybe need a single id's information, you could hit their API too, although this wouldn't work for bulk or at least didn't work for me. You can map the uniprot accession you get from this to PDB or whatever else you need!

import requests
def get_uniprot_accession(geneid, format='list'):
    resp = requests.get(
        "https://www.uniprot.org/uniprot/?query={}&sort=score&format={}".format(geneid, format)).text
    if format == 'list':
        resp = resp.strip()
    return resp
| improve this answer | |
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.