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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, Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists provides a hands-on introduction to Unix, Perl and other tools used in sequence bioinformatics. Relevant biological topics are used throughout Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists 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 Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists 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. Genomics and Bioinformatics: An Introduction to Programming Tools for Life Scientists demonstrates that even simple programs can provide powerful solutions to many complex bioinformatics problems.
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
Tore Samuelsson is a professor in biochemistry and bioinformatics at the Institute of Biomedicine, University of Gothenburg, Sweden. He has been active in bioinformatics research for more than 15 years and has over 10 years' experience of teaching in the field, including the development of web resources for molecular biology and bioinformatics education.
"The book provides a lively and accessible introduction to current research in the life sciences, and it does so in a succinct way by grounding the explanations with simple algorithms expressed in Perl code. As such, the book can be very useful to a general science audience, particularly those with a computer science background, whether established researchers or undergraduate students. The writing is inspiring and engaging, and the inclusion of Perl code makes it easy for readers to apply the knowledge and observe the outcomes."
- Sara Kalvala, Computing Reviews
