BookRöbbe Wünschiers.
Summary: This greatly expanded 2nd edition provides a practical introduction to - data processing with Linux tools and the programming languages AWK and Perl- data management with the relational database system MySQL, and- data analysis and visualization with the statistical computing environment R for students and practitioners in the life sciences. Although written for beginners, experienced researchers in areas involving bioinformatics and computational biology may benefit from numerous tips and tricks that help to process, filter and format large datasets. Learning by doing is the basic concept of this book. Worked examples illustrate how to employ data processing and analysis techniques, e.g. for - finding proteins potentially causing pathogenicity in bacteria, - supporting the significance of BLAST with homology modeling, or- detecting candidate proteins that may be redox-regulated, on the basis of their structure. All the software tools and datasets used are freely available. One section is devoted to explaining setup and maintenance of Linux as an operating system independent virtual machine. The author's experiences and knowledge gained from working and teaching in both academia and industry constitute the foundation for this practical approach.
Contents:
Whetting Your Appetite
Introduction
Content of This Book
Computer & Operating Systems
Unix/Linux
Working with Linux
The First Touch
Working with Files
Remote Connections
Playing with Text and Data Files
Using the Shell
Installing BLAST and ClustalW
Shell Programming
Regular Expressions
Sed
Programming
AWK
Perl
Other Programming Languages
Advanced Data Analysis
Relational Databases with MySQL
The Statistics Suite R
Worked Examples
Genomic Analysis of the Pathogenicity Factors from E. coli Strain O157:H7 and EHEC Strain O104:H4
Limits of BLAST and Homology Modeling
Virtual Sequencing of pUC18c
Querying for Potential Redox-Regulated Enzymes.