Biopython: Tutorial and Cookbook

Python Tools for Computational Molecular Biology

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

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Book Description

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

Chapter 1
Chapter 2
Quick Start - What can you do with Biopython?
Chapter 3
Sequence objects
Chapter 4
Sequence annotation objects
Chapter 5
Sequence Input/Output
Chapter 6
Multiple Sequence Alignment objects
Chapter 7
Chapter 8
BLAST and other sequence search tools
Chapter 9
Accessing NCBI's Entrez databases
Chapter 10
Swiss-Prot and ExPASy
Chapter 11
Going 3D: The PDB module
Chapter 12
Bio.PopGen: Population genetics
Chapter 13
Phylogenetics with Bio.Phylo
Chapter 14
Sequence motif analysis using Bio.motifs
Chapter 15
Cluster analysis
Chapter 16
Supervised learning methods
Chapter 17
Graphics including GenomeDiagram
Chapter 18
Chapter 19
Bio.phenotype: analyse phenotypic data
Chapter 20
Cookbook - Cool things to do with it
Chapter 21
The Biopython testing framework
Chapter 22
Chapter 23
Where to go from here - contributing to Biopython

Book Details

Computer Science
PDF Size
3.0 MB
Open Publication License

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