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Semester Project: Greedy Algorithms and Genome Rearrangements August/17/2012 Name: Xuanyu Hu Professor: Elise de Doncker. Outline. 1. Goals of Semester Project 2. Genome Rearrangement 3. Greedy Algorithms 4. Features of Greedy Algorithms 5. Sorting by Reversals Problem

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  1. Semester Project:Greedy Algorithms and Genome RearrangementsAugust/17/2012Name: Xuanyu HuProfessor: Elise de Doncker

  2. Outline • 1. Goals of Semester Project • 2. Genome Rearrangement • 3. Greedy Algorithms • 4. Features of Greedy Algorithms • 5. Sorting by Reversals Problem • 6. Greedy Algorithms in Genome Rearrangement • 7. Project Testing

  3. Goals • 1. Know the result of Genome Rearrangement • 2. Know what are Greedy Algorithms • 3. Use Greedy Algorithms to solve Genome Rearrangement problem

  4. Genome Rearrangements • Every genome rearrangement results in a change of gene ordering, and a series of these rearrangements can alter the genomic architecture of a species.

  5. Greedy Algorithms • A greedy algorithm is an algorithm that follows the problem solving heuristic of making the locally optimal choice at each stage with the hope of finding a global optimum.

  6. Features of Greedy Algorithms • In many problems, a greedy strategy does not in general produce an optimal solution, but nonetheless a greedy heuristic may yield locally optimal solutions that approximate a global optimal solution in a reasonable time.

  7. Sorting by Reversals Problem • SIMPLEREVERSALSORT(π) • 1 for i ← 1 to n-1 • 2 j ← position of element i in π • 3 if j ≠ i • 4 π ← π * ρ (i, j) • 5 output π • 6 if π is the identity permutation • 7 return

  8. Project Testing 1

  9. Problem • Reversal Distance Problem: Given two permutations π and π', find a series of reversals that transforms π into π'.

  10. Input and output • Input: Permutation π and π' • Output: All of the permutations that it goes through in order to transform π into π' with one line after each reversal and the number of reversals.

  11. Project Testing 2

  12. Project Testing 3

  13. Conclusion and Questions • 1. Goals of Semester Project • 2. Definition of Genome Rearrangement • 3. Greedy Algorithms • 4. Features of Greedy Algorithms • 5. Sorting by Reversals Problem • 6. Greedy Algorithms in Genome Rearrangement • 7. Project Testing

  14. References 1.http://bix.ucsd.edu/bioalgorithms/downloads/code/ 2.http://en.wikipedia.org/wiki/Greedy_algorithm 3.http://en.wikipedia.org/wiki/Greedy_algorithm 4.http://www.personal.kent.edu/~rmuhamma/Algorithms/MyAlgorithms/Greedy/greedyIntro.htm 5.http://www.catonmat.net/blog/mit-introduction-to-algorithms-part-eleven/ 6.http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=11899 7.http://dimacs.rutgers.edu/BMC/TeacherMaterials/Rearrange.pdf 8.http://genome.cshlp.org/content/13/1/37.full 9.http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000128 10.http://lib.bioinfo.pl/courses/view/693 11.http://lib.bioinfo.pl/courses/view/693 12.http://en.wikipedia.org/wiki/Bioinformatics

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