Computing for Biologists: Python Programming and Principles

Preface Meet python Part I. Python versus Pathogens: 1. Computing GC content 2. Pathogenicity islands 3. Open reading frames and genes 4. Finding genes (at last!) Part II. Sequence Alignment and Sex Determination: 5. Recursion 6. The use-it-or-lose-it principle 7. Dictionaries, memoization, and speed 8. Sequence alignments and the evolution of sex chromosomes Part III. Phylogenetic Reconstruction and the Origin of Modern Humans: 9. Representing and working with trees 10. Drawing trees 11. The UPGMA algorithm Part IV. Additional Topics: 12. RNA secondary structure prediction 13. Gene regulatory networks and the maximum likelihood method 14. Birds, bees, and genetic algorithms Where to go from here Index.

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