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Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice

Bioinformatics Biocomputing and Perl: An Introduction to Bioinformatics Computing Skills and Practice

Michael Moorhouse, Paul Barry

ISBN: 978-0-470-02645-8

Sep 2005

506 pages



Bioinformatics, Biocomputing and Perl presents a modern introduction to bioinformatics computing skills and practice. Structuring its presentation around four main areas of study, this book covers the skills vital to the day-to-day activities of today’s bioinformatician. Each chapter contains a series of maxims designed to highlight key points and there are exercises to supplement and cement the introduced material.

Working with Perl presents an extended tutorial introduction to programming through Perl, the premier programming technology of the bioinformatics community. Even though no previous programming experience is assumed, completing the tutorial equips the reader with the ability to produce powerful custom programs with ease.

Working with Data applies the programming skills acquired to processing a variety of bioinformatics data. In addition to advice on working with important data stores such as the Protein DataBank, SWISS-PROT, EMBL and the GenBank, considerable discussion is devoted to using bioinformatics data to populate relational database systems. The popular MySQL database is used in all examples.

Working with the Web presents a discussion of the Web-based technologies that allow the bioinformatics researcher to publish both data and applications on the Internet.

Working with Applications shifts gear from creating custom programs to using them. The tools described include Clustal-W, EMBOSS, STRIDE, BLAST and Xmgrace. An introduction to the important Bioperl Project concludes this chapter and rounds off the book.


1. Setting the Biological Scene.

2. Setting the Technological Scene.


3. The Basics.

4. Places to Put Things.

5. Getting Organised.

6. About Files.

7. Patterns, Patterns and More Patterns.

8. Perl Grabbag.


9. Downloading Datasets.

10. The Protein Databank.

11. Non-redundant Datasets.

12. Databases.

13. Databases and Perl.


14. The Sequence Retrieval System.

15. Web Technologies.

16. Web Automation.


17. Tools and Datasets.

18. Applications.

19. Data Visualisation.

20. Introducing Bioperl.

Appendix: A—F. 


"...such a helpful and relevant book...I am following [an] MSc distance learning course in Bioinformatics...I would have been at a complete loss without your book!" (Susan Tzotzos MSc, PhD, Vienna, Austria)
  • An essential textbook for teaching how to apply Perl in the development of Web databases and automating bioinformatics tasks
  • Focuses on learning Perl as a tool then applying it to bioinformatics problems
  • Teaches readers to create their own customized programs to address specific tasks and to manage complex data structures within those programs
  • Each chapter includes an example illustrating the use of material covered in that chapter and exercises to practise
  • Features maxims and technical notes for easy reference.
  • The book will have an accompanying website with details of source code and other supporting material