Python for Bioinformatics

Python for Bioinformatics

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Programming knowledge is often necessary for finding a solution to a biological problem. Based on the authora€™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.... system should install Biopython 1.49 under Python 2.5 (or resign using executable files and do a manual install to get the last version). Easy Install with easy install Some modules support an alternative installation method called easyinstall. ... For Debian/Ubuntu: $ sudo apt-get install python-setuptools Once installed, Python modules can be installed with: $ sudo ... -q bdist_egg --dist-dir alt; = /tmp/easy_install-23lOQH/pyExcelerator-0.6.0a/egg-dist-tmp-YR3GKH zip_safe flag not set;anbsp;...

Title:Python for Bioinformatics
Author:Sebastian Bassi
Publisher:CRC Press - 2009-09-30


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