ABSTRACT

In today's data driven biology, programming knowledge is essential in turning ideas into testable hypothesis. Based on the author’s extensive experience, Python for Bioinformatics, Second Edition helps biologists get to grips with the basics of software development. Requiring no prior knowledge of programming-related concepts, the book focuses on the easy-to-use, yet powerful, Python computer language.

This new edition is updated throughout to Python 3 and is designed not just to help scientists master the basics, but to do more in less time and in a reproducible way. New developments added in this edition include NoSQL databases, the Anaconda Python distribution, graphical libraries like Bokeh, and the use of Github for collaborative development.

section I|209 pages

Programming

chapter 1|16 pages

Introduction

chapter 2|20 pages

First Steps with Python

chapter 3|30 pages

Basic Programming: Data Types

chapter 4|16 pages

Programming: Flow Control

chapter 5|19 pages

Handling Files

chapter 6|24 pages

Code Modularizing

chapter 7|10 pages

Error Handling

chapter 9|53 pages

Introduction to Biopython

section II|102 pages

Advanced Topics

chapter 10|24 pages

Web Applications

chapter 11|17 pages

XML

chapter 12|30 pages

Python and Databases

chapter 13|14 pages

Regular Expressions

chapter 14|14 pages

Graphics in Python

section III|56 pages

Python Recipes with Commented Source Code

chapter 15|6 pages

Sequence Manipulation in Batch

chapter 17|5 pages

Searching for PCR Primers Using Primer3

chapter 20|6 pages

Inferring Splicing Sites

chapter 21|5 pages

Web Server for Multiple Alignment

chapter 23|6 pages

DNA Mutations with Restrictions