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PSA [Conclusion]

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LSM2241 - Pairwise Sequencing Alignment Presentation's Conclusion

LSM2241 - Pairwise Sequencing Alignment Presentation's Conclusion

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Transcript

  • 1. CONCLUSION- Take home message -
    Matrix Gap opening Gap extension
    Dynamic Programming Needle Water
    Local alignment Global alignment
    Similarity Identity
  • 2. Conclusion
    Pair wise Sequencing Alignment
  • 3. Conclusion
    Pair wise Sequencing Alignment
    ???
    ???
    INPUT
  • 4. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
  • 5. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
  • 6. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    Local
    Global
    Process
  • 7. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    Local
    Global
    Process
    Smith-Waterman algorithm
    Needleman-Wunsch algorithm
    • Types of Algorithm
  • Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    Local
    Global
    Process
    Smith-Waterman algorithm
    Needleman-Wunsch algorithm
    • Types of Algorithm
    • 8. Types of software
    WATER
    NEEDLE
    - Parameters-
  • 9. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    Local
    Global
    Process
    Smith-Waterman algorithm
    Needleman-Wunsch algorithm
    • Types of Algorithm
    • 10. Types of software
    WATER
    NEEDLE
    - Parameters-
    E-DNA or BLOSUM or PAM
    E-DNA or BLOSUM or PAM
    • Types of Matrix
  • Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    Local
    Global
    Process
    Smith-Waterman algorithm
    Needleman-Wunsch algorithm
    • Types of Algorithm
    • 11. Types of software
    WATER
    NEEDLE
    - Parameters-
    E-DNA or BLOSUM or PAM
    E-DNA or BLOSUM or PAM
    • Types of Matrix
    Default: Opening G – 10 Extension G – 0.5
    Note: These settings can be customized accordingly!!!
    • GAP Penalties
  • Conclusion
    INPUT
    • Types of Algorithm
    • 12. Types of software
    • 13. Types of Matrix
    • 14. GAP Penalties
  • Conclusion
    Essence of Dynamic Programming
    INPUT
    • Types of Algorithm
    • 15. Types of software
    • 16. Types of Matrix
    • 17. GAP Penalties
  • Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    PROCESS
    Outcome 1
    OUTPUT
  • 18. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    PROCESS
    Outcome 1
    Outcome 2
    OUTPUT
  • 19. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    PROCESS
    Outcome 1
    Outcome 2
    Outcome 3
    OUTPUT
  • 20. Conclusion
    Pair wise Sequencing Alignment
    DNA
    Protein
    INPUT
    Types of Alignment
    Local
    Global
    Local
    Global
    PROCESS
    Outcome 1
    Outcome 2
    Outcome 3
    Outcome 4
    OUTPUT
    Note: Do look out for Sequence Identity (%) , Similarity (%) and alignment of your input sequences