Semester Project:
Greedy Algorithms and
Genome Rearrangements
August/17/2012
Name: Xuanyu Hu
Professor: Elise de Doncker
Outline
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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
Goals
• 1. Know the result of Genome
Rearrangement
• 2. Know what are Greedy Algorithms
• 3. Use Greedy Algorithms to solve
Genome Rearrangement problem
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.
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.
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.
Sorting by Reversals Problem
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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)
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output π
6 if π is the identity permutation
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return
Project Testing 1
Problem
• Reversal Distance Problem: Given
two permutations π and π', find a
series of reversals that transforms π
into π'.
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.
Project Testing 2
Project Testing 3
Conclusion and Questions
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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
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-parteleven/
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%2Fjourn
al.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