Biopython Tutorial & Cookbook

Named authors: Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczyński.

This is from Biopython 1.85.dev0.

Table of contents:

• Introduction
• Quick Start – What can you do with Biopython?
• Sequence objects
• Sequence annotation objects
• Sequence Input/Output
• Sequence alignments
• Pairwise sequence alignment
• Multiple Sequence Alignment objects
• Pairwise alignments using pairwise2
• BLAST (new)
• BLAST (old)
• BLAST and other sequence search tools
• Accessing NCBI’s Entrez databases
• Swiss-Prot and ExPASy
• Going 3D: The PDB module
• Bio.PopGen: Population genetics
• Phylogenetics with Bio.Phylo
• Sequence motif analysis using Bio.motifs
• Cluster analysis
• Graphics including GenomeDiagram
• KEGG
• Bio.phenotype: analyze phenotypic data
• Cookbook – Cool things to do with it
• The Biopython testing framework
• Where to go from here – contributing to Biopython
• Appendix: Useful stuff about Python
• Bibliography