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    Approximation Algorithms_Mehedi

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    A short note for finding the shortest distance between genomes using Approximation Algorithms.

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    Approximation Algorithms_Mehedi

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    mahbub.rhmn.m
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    A short note for finding the shortest distance between genomes using Approximation Algorithms.

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    © © All Rights Reserved

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    A short note for finding the shortest distance between genomes using Approximation Algorithms.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    0 views4 pages

    Approximation Algorithms_Mehedi

    Uploaded by

    mahbub.rhmn.m
    A short note for finding the shortest distance between genomes using Approximation Algorithms.

    Copyright:

    © All Rights Reserved
    Download as DOCX, PDF, TXT or read online from Scribd
    Download as docx, pdf, or txt
    You are on page 1of 4

    Approximation Algorithms

    An Approximation Algorithm for Sorting by Reversals and


    Transpositions

    What is the Approximation algorithm?


    Approximation algorithms are designed to solve problems not solvable in
    polynomial time for approximate solutions. These problems are known as
    NP-complete problems. These problems are significantly effective in
    solving real-world problems, therefore, it becomes important to solve them
    using a different approach.

    NP-complete problems can still be solved in three cases:

    1. the input could be so small that the execution time is reduced


    2. some problems can still be classified into problems that can be solved
    in polynomial time
    3. use approximation algorithms to find near-optima solutions for
    the problems.

    Performance Ratios
    The main idea behind calculating the performance ratio of an
    approximation algorithm also called an approximation ratio, is to find how
    close the approximate solution is to the optimal solution.

    The approximate ratio is represented using ρ(n) where n is the input size of
    the algorithm, C is the near-optimal solution obtained by the algorithm, and
    C* is the optimal solution for the problem. The algorithm has an approximate
    ratio of ρ(n) if and only if −

    max{C/C∗,C∗/C}≤ρ(n)
    The algorithm is then called a ρ(n)-approximation algorithm.

    Example:

    Advantages:

    Disadvantages:
    Genome rearrangements:

    Genome rearrangements are mutations that change the gene content of a


    genome or the arrangement of the genes on a genome.

    combinatorial problem:

    A combinatorial problem consists in, given a finite collection of objects and a set
    of constraints, finding an object of the collection that satisfies all constraints (and
    possibly that optimizes some objective function).

    Reversal, which inverts the order and the orientation of the genes inside
    a segment of the genome.

    Transposition, that moves a segment of the genome to another position.

    (4 – 2/k)-approximation algorithm for sorting by reversals and


    transpositions.
    Proving an upper bound means you have proven that the algorithm will
    use no more than some limit on a resource.
    Proving a lower bound means you have proven that the algorithm will use no
    less than some limit on a resource.
    "Resource" in this context could be time, memory, bandwidth, or something
    else.
    Sorting by Reversals and Transpositions

    Let,

    π = [π0 π1 π2 ... πn πn+1] ; n+2 distinct elements

    Adjacent

    if, |πi −πi+1| = 1

    Breakpoints

    Two elements πi and πi+1 of π for all 0 ≤ i ≤ n are called adjacent if |πi
    −πi+1| = 1. Otherwise there is said to be a breakpoint between the two
    elements. We denote the total number of breakpoints in π by b(π).

    Cycle Decomposition Graph

    The cycle decomposition graph G(π) is an undirected multigraph whose


    n+2 vertices are πi for 0 ≤ i ≤ n+1. G(π) has 2(n+1) edges and they are of
    two types: gray and black. For each 0 ≤ i ≤ n, the vertices πi and πi+1 are
    joined by a black edge.For 0≤i,j≤n+1, there is a gray edge between πi and
    πj iff πi = πj + 1.
    A graph in which multiple edges may connect the same pair of vertices is
    called a multigraph.

    Cycle Decomposition Graph

    A cycle C is semi-oriented if there exist two black edges such that


    along the boundary of C one is traversed left to right and the
    other one is traversed right to left

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