Notebooks-Bioinformatics

Introduction

This repository contains iPython notebooks that can be run using Project Jupyter, covering topics relating to bioinformatics.

Contents

Biopython

• Biopython: KGML - an introduction to Biopython's Bio.KEGG.REST and Bio.KEGG.KGML modules for downloading, interacting with, and rendering custom graphics from KEGG data. <img src="images/kgml.png",width=120 />
• Biopython: NCBI/Entrez - an introduction to downloading genome data from NCBI using Biopython's Bio.Entrez module. <img src="images/entrez.png",width=120 /> </ul>

Comparative Genomics

• Reciprocal Best Hits - an introduction to reciprocal best hits, a method for identifying "equivalent features" (putative orthologues) across two or more genomes. <img src="images/rbbh.png",width=120 />

Statistics

• The Baserate Fallacy - interactive graphical examples describing the baserate fallacy, centred around functional prediction of effectors in bacterial pathogens. <img src="images/baserate.png",width=120 />