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    Aamena Yusuf
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    The document discusses the Smith-Waterman algorithm for local sequence alignment. It introduces two key differences from the Needleman-Wunsch global alignment algorithm: 1) the maximum value F(i,j) can be 0, allowing alignments to end anywhere in the matrix, and 2) it uses the same three recurrence relations as Needleman-Wunsch but includes F(i,j)=0. An example application compares two protein sequences and identifies the optimal local alignment using a BLOSUM scoring matrix and linear gap penalty.

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    The document discusses the Smith-Waterman algorithm for local sequence alignment. It introduces two key differences from the Needleman-Wunsch global alignment algorithm: 1) the maximum value F(i,j) can be 0, allowing alignments to end anywhere in the matrix, and 2) it uses the same three recurrence relations as Needleman-Wunsch but includes F(i,j)=0. An example application compares two protein sequences and identifies the optimal local alignment using a BLOSUM scoring matrix and linear gap penalty.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    12 views4 pages

    Lecture 7 PDF

    Uploaded by

    Aamena Yusuf
    The document discusses the Smith-Waterman algorithm for local sequence alignment. It introduces two key differences from the Needleman-Wunsch global alignment algorithm: 1) the maximum value F(i,j) can be 0, allowing alignments to end anywhere in the matrix, and 2) it uses the same three recurrence relations as Needleman-Wunsch but includes F(i,j)=0. An example application compares two protein sequences and identifies the optimal local alignment using a BLOSUM scoring matrix and linear gap penalty.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
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    Unit No: 1: Pairwise Sequence Analysis

    Lecture No: 7
    Dynamic Programming
    Approach- Smith-Waterman
    Algorithm problem solving
    Smith and Waterman (local alignment)

    Two differences:

    0
    1.
    F(i, j) = F(i-1, j-1) + s(xi ,yj)
    F(i, j) = max
    F(i, j) = F(i-1, j) - d
    F(i, j) = F(i, j-1) - d
    2. An alignment can now end anywhere in the matrix

    Example:
    Sequence 1 HEAGAWGHE E
    Sequence 2 PAW H EAE
    Scoring parameters: BLOSUM
    Gap penalty: Linear gap penalty of 8

    2 Lecture 7 – Smith-Waterman Algorithm problem solving


    Smith Waterman alignment

    3 Lecture 7 – Smith-Waterman Algorithm problem solving


    Thank You

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