Finding a protein in multiple databases

Before we start performing some more structural biology, we will see how to 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 06_Prot/Intro.ipynb notebook.

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()
       return...