Python for bioinformatics / Sebastian Bassi. — Boca Raton, Fla. ; London : Chapman & Hall/CRC, c2010. – (58.17115/B321) |
Contents
Contents
List of Tables
List of Figures
Preface
Acknowledgments
I Programming
1 Introduction
2 First Steps with Python
3 Basic Programming: Data Types
4 Programming: Flow Control
5 Dealing with Files
6 Code Modularizing
7 Error Handling
8 Introduction to Object Orienting Programming (OOP)
9 Regular Expressions
II Bioppython
10 Introduction to Biopython
III Advanced Topics
Contents
11 Web Applications
12 XML
13 Python and Databases
14 Collaborative Development: Version Control
IV Python Recipes with Commented Source Code 315
15 Sequence Manipulation in Batch
16 Web Application for Filtering Vector Contamination
17 Searching for PCR Primers Using Primer3
18 Calculating Melting Temperature from a Set of Primers
19 Filtering Out Specific Fields from a Genbank File
20 Converting XML BLAST File into HTML 341
21 Infering Splicing Sites
22 DNA Mutations with Restrictions
23 Web Server for Multiple Alignment 373
24 Drawing Marker Positions Using Data Stored in a Database 379
A Python and Biopython Installation
B Selected Papers
C Included DVD: Virtual Machine Installation and Use
D Python Language Reference 457
E Answers to Odd-Numbered Questions
F Python Style Guide
Index