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1 - Introduction: working with the molecules of life in the computer

Published online by Cambridge University Press:  05 August 2012

Tore Samuelsson
Affiliation:
Göteborgs Universitet, Sweden
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Summary

[Jim Kent] embarked on a four-week programming marathon, icing his wrists at night to prevent them from seizing up as he churned out computer code by day. His deadline was June 26, when the completion of the rough draft was to be announced.

(DNA: The Secret of Life, describing Jim Kent's efforts in the human genome sequencing project in 2000; Watson and Berry, 2003)

It was a somewhat historic event when President Bill Clinton announced, on 26 June 2000, the completion of the first survey of the entire human genome. We were able for the first time to read all three billion letters of the human genetic make-up. This information was the ground-breaking result of the Human Genome Project. The success of this project relied on advanced technology, such as a number of experimental molecular biology methods. However, it also required a significant contribution from more theoretical disciplines such as computer science. Thus, in the final phase of the project, numerous pieces of information like those in a giant jigsaw puzzle needed to be appropriately combined. This step was critically dependent on programming efforts. Adding further tension to the programming exercises was the fact that a private company, Celera, was competing with the academic Human Genome Project. This competition was sometimes referred to as ‘the Genome War’ (Shreeve, 2004). While computationally talented people like Jim Kent ‘churned out computer code’, other gifted bioinformaticians, such as Gene Myers at Celera, worked on related jigsaw-puzzle problems. Ideally, scientists should not war against each other; however, there was an important conclusion from these projects in which important genetic information was generated: computing is an essential part of biological research.

Type
Chapter
Information
Genomics and Bioinformatics
An Introduction to Programming Tools for Life Scientists
, pp. 1 - 18
Publisher: Cambridge University Press
Print publication year: 2012

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References

Dobzhansky, T 1964 Biology, molecular and organismic Am Zool 4 443 CrossRefGoogle ScholarPubMed
International Human Genome Sequencing Consortium 2004 Finishing the euchromatic sequence of the human genome Nature 431 931 CrossRefGoogle Scholar
Lander, E. S Linton, L. M Birren, B 2001 Initial sequencing and analysis of the human genome Nature 409 860 Google ScholarPubMed
Pettersen, E. F Goddard, T. D Huang, C. C 2004 UCSF Chimera: a visualization system for exploratory research and analysis J Comput Chem 25 1605 CrossRefGoogle ScholarPubMed
Shreeve, J 2004 The Genome War: How Craig Venter Tried to Capture the Code of Life and Save the World New York Alfred A. Knopf Google Scholar
Venter, J. C Adams, M. D Myers, E. W 2001 The sequence of the human genome Science 291 1304 CrossRefGoogle ScholarPubMed
Watson, J. D Berry, A 2003 DNA: The Secret of Life New York Alfred A. Knopf Google Scholar
Watson, J. D Crick, F. H 1953 Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid Nature 171 737 CrossRefGoogle ScholarPubMed

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