Install

You can easily install PyCoM using pip from the source code on github respository.

pip3 install git+https://github.com/scdantu/pycom

Differences

You can work with PyCoMdb in three different modes:

  1. PyCoM (local): Download the database to your computer and use PyCoM.

  2. PyCoM (remote): Work with the database on PyCoM server using PyCoM.

  3. WebAPI: Work with the WebAPI without using PyCoM.

Using PyCoM (local) allows access to all the functional features, while PyCoM (remote) and the WebAPI has some limitations as shown in the table below:

Functionality

PyCoM Library

===================+=======================================

Database is Local | Remote database on pycom.brunel.ac.uk

Web API

Query the database

Y

Y

Y

Load matrices

Y

Y

Y

Display basic properties of each entry1

Y

Y

Y

Provides access to

Y

N

N

1.     Diseases

2.     CATH

3.     EC ID

4.     PDB id list

5.     Organism taxonomy

6.     Substrates list

7.     List of Cofactors

8.     PTM’s

9.     List of Ligands

10.  Molecular functions

11.  biological processes

12.  cellular components

13.  protein domain

14.  coding sequence diversity

15.  developmental stage