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?
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