Python for Bioinformatics

Couverture
CRC Press, 19 avr. 2016 - 587 pages

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.

 

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Table des matières

Introduction
3
First Steps with Python
19
Basic Programming Data Types
39
Programming Flow Control
71
Dealing with Files
87
Code Modularizing
105
Error Handling
125
Introduction to Object Orienting Programming OOP
139
Sequence Manipulation in Batch
317
Searching for PCR Primers Using Primer3
329
Calculating Melting Temperature from a Set of Primers
335
Converting XML BLAST File into HTML
341
DNA Mutations with Restrictions
367
Web Server for Multiple Alignment
373
Drawing Marker Positions Using Data Stored in a Database
379
Python and Biopython Installation
393

Regular Expressions
159
Biopython
173
Introduction to Biopython
175
Web Applications
225
XML
249
Python and Databases
269
Collaborative Development Version Control
297
Python Recipes with Commented Source Code
315
Selected Papers
409
Included DVD Virtual Machine Installation and Use
449
Python Language Reference
457
Answers to OddNumbered Questions
539
Python Style Guide
553
Index
577
Back cover
585
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À propos de l'auteur (2016)

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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