Biopython Tutorial and Cookbook

Biopython Tutorial and Cookbook by Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczyn´ski

Python is an object oriented, interpreted, flexible language that is becoming increasingly popular for scientific computing. Python is easy to learn, has a very clear syntax and can easily be extended with modules written in C, C++ or FORTRAN.

The main Biopython releases have lots of functionality, including:

The ability to parse bioinformatics files into Python utilizable data structures, including support for the following formats:

- Blast output - both from standalone and WWW Blast
Clustalw
- FASTA
- GenBank
- PubMed and Medline
- ExPASy files, like Enzyme and Prosite
- SCOP, including 'dom' and 'lin' files
- UniGene
- SwissProt

Files in the supported formats can be iterated over record by record or indexed and accessed via a
Dictionary interface.

Code to deal with popular on-line bioinformatics destinations such as:
NCBI - Blast, Entrez and PubMed services
- ExPASy - Swiss-Prot and Prosite entries, as well as Prosite searches
Interfaces to common bioinformatics programs such as:
Standalone Blast from NCBI
- Clustalw alignment program
- EMBOSS command line tools