This tutorial shows how to obtain multiple sequence alignments (MSA) from Pfam, how to manipulate MSA files, and obtain conservation and coevolution patterns.

Required Programs

Latest version of ProDy and Matplotlib required.

Getting Started

To follow this tutorial, you will need the following files:

There are no required files.

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy and Matplotlib packages.

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

We have included these imports in every part of the tutorial, so that code copied from the online pages is complete. You do not need to repeat imports in the same Python session.