Python for Bioinformatics

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.

Table of Contents

Part I: Programming
Chapter 1: Introduction
Chapter 2: First Steps with Python
Chapter 3: Basic Programming: Data Types
Chapter 4: Programming: Flow Control
Chapter 5: Dealing with Files
Chapter 6: Code Modularizing
Chapter 7: Error Handling
Chapter 8: Introduction to Object Orienting Programming (OOP)
Chapter 9: Regular Expressions

Part II: Biopython
Chapter 10: Introduction to Biopython

Part III: Advanced Topics
Chapter 11: Web Applications
Chapter 12: XML
Chapter 13: Python and Databases
Chapter 14: Collaborative Development: Version Control

Part IV: Python Recipes with Commented Source Code
Chapter 15: Sequence Manipulation in Batch
Chapter 16: Web Application for Filtering Vector Contamination
Chapter 17: Searching for PCR Primers Using Primer3
Chapter 18: Calculating Melting Temperature from a Set of Primers
Chapter 19: Filtering Out Specific Fields from a Genbank File
Chapter 20: Converting XML BLAST File into HTML
Chapter 21: Infering Splicing Sites
Chapter 22: DNA Mutations with Restrictions
Chapter 23: Web Server for Multiple Alignment
Chapter 24: 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