Python for Bioinformatics

Description

Programming knowledge is often necessary for finding a solution to a biological problem. Based on the author’s experience working for an agricultural biotechnology company, Python for Bioinformatics helps scientists solve their biological problems by helping them understand the basics of programming. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.

The book begins with a very basic introduction that teaches the principles of programming. It then introduces the Biopython package, which can be useful in solving life science problems. The next section covers sophisticated tools for bioinformatics, including relational database management systems and XML. The last part illustrates applications with source code, such as sequence manipulation, filtering vector contamination, calculating DNA melting temperature, parsing a genbank file, inferring splicing sites, and more. The appendices provide a wealth of supplementary information, including instructions for installing Python and Biopython and a Python language and style guide.

By incorporating examples in biology as well as code fragments throughout, the author places a special emphasis on practice, encouraging readers to experiment with the code. He shows how to use Python and the Biopython package for building web applications, genomic annotation, data manipulation, and countless other applications.

Reviews

The book will be helpful for its intended audience. Numerous code fragments in the book will be beneficial for biologists who are unfamiliar with programming. Readers can try out, test, and modify the code to suit their needs. … a useful introduction to the topic. The style of presentation is good, and the code samples are worthwhile. … I strongly recommend this book as a useful reference for computational biologists, programmers, and bioinformatics specialists (students as well as researchers).

—Computing Reviews, November 2011

Contents

PROGRAMMING

Introduction

First Steps with Python

Basic Programming: Data Types

Programming: Flow Control

Dealing with Files

Code Modularizing

Error Handling

Introduction to Object Orienting Programming (OOP)

Regular Expressions

BIOPYTHON

Introduction to Biopython

ADVANCED TOPICS

Web Applications

XML

Python and Databases

Collaborative Development: Version Control

PYTHON RECIPES WITH COMMENTED SOURCE CODE

Sequence Manipulation in Batch

Web Application for Filtering Vector Contamination

Searching for PCR Primers Using Primer3

Calculating Melting Temperature from a Set of Primers

Filtering out Specific Fields from a Genbank File

Converting XML Blast File into HTML

Inferring Splicing Sites

DNA Mutations with Restrictions

Web Server for Multiple Alignment

Drawing Marker Positions Using Data Stored in a Database

Appendix A: Python and Biopython Installation

Appendix B: Selected Papers

Appendix C: Included DVD: Virtual Machine Installation and Use

Appendix D: Python Language Reference

Appendix E: Answers to Odd-Numbered Questions

Appendix F: Python Style Guide

Index

Author Bio

Sebastian Bassi is the leader of the DNALinux bioinformatics distribution and member of the developer team for Biopython. He is currently providing bioinformatics support for the tomato mitochondrial genome sequencing project, which is part of the Latin America Solanaceae Genome Project (LAT-SOL).

Related Subjects

1. Molecular Biology
2. Bioinformatics