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    Dynamic Programming: Longest Common Subsequences

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    yetsedaw
    The document discusses the longest common subsequence problem and presents a dynamic programming algorithm to solve it in quadratic time. It describes how the algorithm works by building up a table L where L[i,j] represents the length of the LCS of the prefixes X[0..i] and Y[0..j]. It can find the LCS and run in O(nm) time where n and m are the lengths of the input strings.

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    Dynamic Programming: Longest Common Subsequences

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    yetsedaw
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    The document discusses the longest common subsequence problem and presents a dynamic programming algorithm to solve it in quadratic time. It describes how the algorithm works by building up a table L where L[i,j] represents the length of the LCS of the prefixes X[0..i] and Y[0..j]. It can find the LCS and run in O(nm) time where n and m are the lengths of the input strings.

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    The document discusses the longest common subsequence problem and presents a dynamic programming algorithm to solve it in quadratic time. It describes how the algorithm works by building up a table L where L[i,j] represents the length of the LCS of the prefixes X[0..i] and Y[0..j]. It can find the LCS and run in O(nm) time where n and m are the lengths of the input strings.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    22 views11 pages

    Dynamic Programming: Longest Common Subsequences

    Uploaded by

    yetsedaw
    The document discusses the longest common subsequence problem and presents a dynamic programming algorithm to solve it in quadratic time. It describes how the algorithm works by building up a table L where L[i,j] represents the length of the LCS of the prefixes X[0..i] and Y[0..j]. It can find the LCS and run in O(nm) time where n and m are the lengths of the input strings.

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    You are on page 1of 11

    Presentation for use with the textbook, Algorithm Design and

    Applications, by M. T. Goodrich and R. Tamassia, Wiley, 2015

    Dynamic Programming:
    Longest Common Subsequences

    © 2015 Goodrich and Tamassia LCS 1


    Application: DNA Sequence
    Alignment
    DNA sequences can be viewed as strings of
    A, C, G, and T characters, which represent
    nucleotides.
    Finding the similarities between two DNA
    sequences is an important computation
    performed in bioinformatics.
    n  For instance, when comparing the DNA of
    different organisms, such alignments can highlight
    the locations where those organisms have
    identical DNA patterns.

    © 2015 Goodrich and Tamassia LCS 2


    Application: DNA Sequence
    Alignment
    Finding the best alignment between two DNA strings
    involves minimizing the number of changes to
    convert one string to the other.

    A brute-force search would take exponential time,


    but we can do much better using dynamic
    programming.
    © 2015 Goodrich and Tamassia LCS 3
    The General Dynamic
    Programming Technique
    Applies to a problem that at first seems to
    require a lot of time (possibly exponential),
    provided we have:
    n  Simple subproblems: the subproblems can be
    defined in terms of a few variables, such as j, k, l,
    m, and so on.
    n  Subproblem optimality: the global optimum value
    can be defined in terms of optimal subproblems
    n  Subproblem overlap: the subproblems are not
    independent, but instead they overlap (hence,
    should be constructed bottom-up).

    © 2015 Goodrich and Tamassia LCS 4


    Subsequences
    A subsequence of a character string
    x0x1x2…xn-1 is a string of the form xi xi …
    1 2

    xi , where ij < ij+1.


    k

    Not the same as substring!


    Example String: ABCDEFGHIJK
    n  Subsequence: ACEGJIK
    n  Subsequence: DFGHK

    n  Not subsequence: DAGH

    © 2015 Goodrich and Tamassia LCS 5


    The Longest Common
    Subsequence (LCS) Problem
    Given two strings X and Y, the longest
    common subsequence (LCS) problem is
    to find a longest subsequence common
    to both X and Y
    Has applications to DNA similarity
    testing (alphabet is {A,C,G,T})
    Example: ABCDEFG and XZACKDFWGH
    have ACDFG as a longest common
    subsequence

    © 2015 Goodrich and Tamassia LCS 6


    A Poor Approach to the
    LCS Problem
    A Brute-force solution:
    n  Enumerate all subsequences of X
    n  Test which ones are also subsequences of Y

    n  Pick the longest one.

    Analysis:
    n  If X is of length n, then it has 2n
    subsequences
    n  This is an exponential-time algorithm!

    © 2015 Goodrich and Tamassia LCS 7


    A Dynamic-Programming
    Approach to the LCS Problem
    Define L[i,j] to be the length of the longest common
    subsequence of X[0..i] and Y[0..j].
    Allow for -1 as an index, so L[-1,k] = 0 and L[k,-1]=0, to
    indicate that the null part of X or Y has no match with the
    other.
    Then we can define L[i,j] in the general case as follows:
    1.  If xi=yj, then L[i,j] = L[i-1,j-1] + 1 (we can add this match)

    2.  If xi≠yj, then L[i,j] = max{L[i-1,j], L[i,j-1]} (we have no


    match here)
    Case 1: Case 2:

    © 2015 Goodrich and Tamassia LCS 8


    An LCS Algorithm
    Algorithm LCS(X,Y ):
    Input: Strings X and Y with n and m elements, respectively
    Output: For i = 0,…,n-1, j = 0,...,m-1, the length L[i, j] of a longest string
    that is a subsequence of both the string X[0..i] = x0x1x2…xi and the
    string Y [0.. j] = y0y1y2…yj
    for i =1 to n-1 do
    L[i,-1] = 0
    for j =0 to m-1 do
    L[-1,j] = 0
    for i =0 to n-1 do
    for j =0 to m-1 do
    if xi = yj then
    L[i, j] = L[i-1, j-1] + 1
    else
    L[i, j] = max{L[i-1, j] , L[i, j-1]}
    return array L
    © 2015 Goodrich and Tamassia LCS 9
    Visualizing the LCS Algorithm

    © 2015 Goodrich and Tamassia LCS 10


    Analysis of LCS Algorithm
    We have two nested loops
    n  The outer one iterates n times
    n  The inner one iterates m times

    n  A constant amount of work is done inside


    each iteration of the inner loop
    n  Thus, the total running time is O(nm)

    Answer is contained in L[n,m] (and the


    subsequence can be recovered from the
    L table).

    © 2015 Goodrich and Tamassia LCS 11

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