Finding a protein in multiple databases

Before we start performing some more structural biology, we will look at how we can access existing proteomic databases, such as UniProt. We will query UniProt for our gene of interest, TP53, and take it from there.

Getting ready

To access data, we will use Biopython and the REST API (we used a similar approach in Chapter 3, Working with Genomes) with the requests library to access web APIs. The requests API is an easy-to-use wrapper for web requests that can be installed using standard Python mechanisms (for example, pip and conda). You can find this content in the Chapter07/Intro.ipynb Notebook file.

How to do it...

Take a look at the following steps:

1. First, let's define a function to perform REST queries on UniProt, as follows:

import requests
server = 'http://www.uniprot.org/uniprot'
def do_request(server, ID='', **kwargs):
    params = ''
    req = requests.get('%s/%s%s' % (server, ID, params), params=kwargs)
    if not req.ok:
        req.raise_for_status...