Biopython Tutorial and Cookbook

Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck

Last Update--2 July 2006

• Table of Contents
• Introduction
  • What is Biopython?
  • Installing Biopython
  • FAQ
• Quick Start -- What can you do with Biopython?
  • General overview of what Biopython provides
  • Working with sequences
  • A usage example
  • Parsing biological file formats
  • Connecting with biological databases
  • What to do next
• Cookbook -- Cool things to do with it
  • BLAST
  • SWISS-PROT
  • PubMed
  • GenBank
  • Dealing with alignments
  • Substitution Matrices
  • More Advanced Sequence Classes -- Sequence IDs and Features
  • BioRegistry -- automatically finding sequence sources
  • BioSQL -- storing sequences in a relational database
  • BioCorba
  • Going 3D: The PDB module
  • Miscellaneous
• Advanced
  • Sequence Class
  • Regression Testing Framework
  • Parser Design
  • Substitution Matrices
• Where to go from here -- contributing to Biopython
  • Maintaining a distribution for a platform
  • Bug Reports + Feature Requests
  • Contributing Code
• Appendix: Useful stuff about Python
  • What the heck in a handle?

This document was translated from L^AT_EX by H^EV^EA and H^AC^HA.