The Biopython Project is an international association of developers tools for computational molecular biology. Python is an object oriented, interpreted,flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, hasa very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.
Thegoal of Biopython is to make it as easy as possible to use Python for bioinformatics by creating high-quality, reusable modules and classes.
Biopython features include parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,...), access to online services (NCBI, Expasy,...), interfaces to commonand not-so-common programs (Clustalw, DSSP, MSMS...), a standard sequence class, various clusteringmodules, a KD tree data structure etc.
This open book is licensed under a Open Publication License (OPL). You can download Biopython: Tutorial and Cookbook ebook for free in PDF format (3.0 MB).
Table of Contents
Quick Start - What can you do with Biopython?
Sequence annotation objects
Multiple Sequence Alignment objects
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
Supervised learning methods
Graphics including GenomeDiagram
Bio.phenotype: analyse phenotypic data
Cookbook - Cool things to do with it
The Biopython testing framework
Where to go from here - contributing to Biopython