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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

By : Tiago R Antao, Tiago Antao
4.7 (6)
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Bioinformatics with Python Cookbook

Bioinformatics with Python Cookbook

4.7 (6)
By: Tiago R Antao, Tiago Antao

Overview of this book

If you have intermediate-level knowledge of Python and are well aware of the main research and vocabulary in your bioinformatics topic of interest, this book will help you develop your knowledge further.
Table of Contents (11 chapters)
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10
Index

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...

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