Books  Data Analysis & Modelling  Bioinformatics 

Python for Bioinformatics

By: Sebastian Bassi

584 pages, no illustrations

Chapman & Hall (CRC Press)

Paperback | Oct 2009 | #171395 | ISBN-13: 9781584889298
Availability: Usually dispatched within 6 days Details
NHBS Price: £55.99 $71/€66 approx

About this book

Python is a popular computer language used in a wide range of applications, from peer-to-peer software to dynamic generated web pages. Python for Bioinformatics provides an accessible introduction to both the Python and BioPython languages. The book addresses advanced topics, from web applications and XML to databases and version control. In addition to useful appendices with reference material on biological file formats, the book presents commented working code and new programming techniques, such as error handling, functions, and modules. It also includes source code as well as a companion CD-ROM that contains a virtual machine with complete installation and a working web server.


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

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Biography

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).

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