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    Sequence Alignment II

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    Lucky Lokesh
    1) The document discusses sequence alignment techniques including dynamic programming, alignment graphs, the Needleman-Wunsch algorithm, and local vs. global alignment. 2) It explains how to construct an alignment graph and select the best pathway by scoring each option and choosing the one with the highest score. 3) The Needleman-Wunsch algorithm uses dynamic programming to initialize a matrix and fill it to find the optimal alignment score and then back trace to obtain the alignment.

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    Sequence Alignment II

    Uploaded by

    Lucky Lokesh
    20 views19 pages
    1) The document discusses sequence alignment techniques including dynamic programming, alignment graphs, the Needleman-Wunsch algorithm, and local vs. global alignment. 2) It explains how to construct an alignment graph and select the best pathway by scoring each option and choosing the one with the highest score. 3) The Needleman-Wunsch algorithm uses dynamic programming to initialize a matrix and fill it to find the optimal alignment score and then back trace to obtain the alignment.

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    Sequence alignment II

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    1) The document discusses sequence alignment techniques including dynamic programming, alignment graphs, the Needleman-Wunsch algorithm, and local vs. global alignment. 2) It explains how to construct an alignment graph and select the best pathway by scoring each option and choosing the one with the highest score. 3) The Needleman-Wunsch algorithm uses dynamic programming to initialize a matrix and fill it to find the optimal alignment score and then back trace to obtain the alignment.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Flag for inappropriate content
    Download as pdf or txt
    20 views19 pages

    Sequence Alignment II

    Uploaded by

    Lucky Lokesh
    1) The document discusses sequence alignment techniques including dynamic programming, alignment graphs, the Needleman-Wunsch algorithm, and local vs. global alignment. 2) It explains how to construct an alignment graph and select the best pathway by scoring each option and choosing the one with the highest score. 3) The Needleman-Wunsch algorithm uses dynamic programming to initialize a matrix and fill it to find the optimal alignment score and then back trace to obtain the alignment.

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    © All Rights Reserved
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    Flag for inappropriate content
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    of 19

    Bioinformatics

    Prof. M. Michael Gromiha


    Department of Biotechnology
    Indian Institute of Technology, Madras

    Lecture - 7b
    Sequence Alignment II

    Dynamic Programming

    Sequence Alignment
    Alignment Graph

    This graph shows that the vertical and horizontal lines represents gap and diagonal lines represents
    match and mismatch.
    Constructing graphic representation of alignment
    Pathway of an alignment

    The alignment can be obtained by multiple pathways represented by following graphs.


    Best Pathway Selection

    Scoring Function

    The best pathway can be obtained by scoring each pathway and selecting the one with highest
    score.
    Alignment score calculation
    Needleman-Wunsch Algorithm
    Initialization of matrix

    Matrix filling
    Optimal Score

    Back tracing to find the alignment


    Types of alignment
    Semi-global alignment

    Local alignment
    Local alignment scoring scheme

    Matrix initialization
    Matrix filling
    Back tracing to find the alignment

    Local sequence alignment (Example 2)


    Matrix initialization

    Matrix filling and back tracing

    In this way sequence alignment can help us to obtain a specific motif in the two sequences.

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