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Bioinformatics CSM17 Week 7: Simulations:

Explore genetic algorithms and evolutionary computation in bioinformatics simulations, including the use of artificial chromosomes to simulate sexual reproduction and evolution. Learn about mitosis, meiosis, mutation, crossover, and the main features of GAs. Discover a simple example of population selection and survival, as well as the effects of mutation. Also, discover useful websites and references for further study.

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Bioinformatics CSM17 Week 7: Simulations:

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  1. Bioinformatics CSM17 Week 7: Simulations: • Genetic Algorithms • Evolutionary Computation JYC: CSM17

  2. Genetic Algorithms (GAs) • simulate sexual reproduction • use artificial ‘chromosomes’ • simulate evolution JYC: CSM17

  3. ‘Real’ Chromosomes • humans have 46 in total • 23 homologous pairs • half from each parent JYC: CSM17

  4. Mitosis • normal cell division e.g. for growth, repair • all cells are diploid (usually) • i.e. they are said to be ‘2n’ JYC: CSM17

  5. Meiosis • cell division to produce gametes • gametes • Female: eggs or ova (singular ovum) • Male: sperm • daughter cells are haploid (n) JYC: CSM17

  6. Main features of GAs • crossover (chiasma) • ‘chromosomes’ • population containing individuals • successive generations • survival of the ‘fittest’ • only the ‘most fitted’ reproduce • (removal of the worst) • mutation JYC: CSM17

  7. A Simple Example • population of 4 • attributes are simple numbers • fitness function is a minimisation function • only 2 best fitted survive to reproduce JYC: CSM17

  8. Mutation • changes of nucleotide bases • caused by • ionizing radiation, mutagenic chemicals • usually harmful (damaging) • may be • single base (changing one amino acid) • frameshift (more serious) JYC: CSM17

  9. Karl Sims • Evolved creatures • Swimming • Jumping • Walking • Following....etc. JYC: CSM17

  10. Useful Websites • Evolutionary design by computers: http://www.cs.ucl.ac.uk/staff/P.Bentley/evdes.html • Evolving creatures (Karl Sims): http://www.genarts.com/karl/evolved-virtual-creatures.html • Creature Labs (Creatures) http://www.gamewaredevelopment.co.uk/ creatures_index.php JYC: CSM17

  11. References & Bibliography • Bentley, P. (ed). Evolutionary design by computers, Morgan Kaufmann. ISBN: 155860605X • Mitchell, M. (1996). An introduction to genetic algorithms. MIT Press, Cambridge, USA. ISBN 0-262-13316-4 • Gibas & Jambeck (2001). Bioinformatics Computer Skills. p401. • Fogel, G. B. & Corne, D. W. (eds.). (2003) Evolutionary computation in bioinformatics. Morgan Kaufmann. ISBN 1-55860-797-8 JYC: CSM17

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