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With the arrival of genomics and genome sequencing projects, biology has been transformed into an incredibly data-rich science. The vast amount of information generated has made computational analysis critical and has increased demand for skilled bioinformaticians. Designed for biologists without previous programming experience, this textbook provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout the book and are combined with practical bioinformatics examples, leading students through the process from biological problem to computational solution. All of the Perl scripts, sequence and database files used in the book are available for download at the accompanying website, allowing the reader to easily follow each example using their own computer. Programming examples are kept at an introductory level, avoiding complex mathematics that students often find daunting. The book demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.

Table of Contents

 

Preface

Acknowledgements

Design and conventions of this book

1. Introduction – working with the molecules of life in the computer

2. Gene technology – cutting DNA

3. Gene technology – knocking genes down

4. Gene technology – amplifying DNA

5. Human disease – when DNA sequences are toxic

6. Human disease – iron imbalance and the iron responsive element

7. Human disease – cancer as a result of aberrant proteins

8. Evolution – what makes us human?

9. Evolution – resolving a criminal case

10. Evolution – the sad case of the Tasmanian tiger

11. A function to every gene – termites, metagenomics and learning about the function of a sequence

12. A function to every gene – royal blood and order in the sequence universe

13. A function to every gene – a slimy molecule

14. Information resources – learning about flu viruses

15. Finding genes – going ashore at CpG islands

16. Finding genes – in the world of snurps

17. Finding genes – hunting for the distant RNA relatives

18. Personal genomes – the differences between you and me

19. Personal genomes – what's in my genome?

20. Personal genomes – details of family genetics

Appendix I. Brief Unix reference

Appendix II. A selection of biological sequence analysis software

Appendix III. Short Perl reference

Appendix IV. Brief introduction to R

Index.