PSA [Conclusion]
description
Transcript of PSA [Conclusion]
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CONCLUSION- Take home message -
Matrix Gap opening Gap extension Dynamic Programming Needle Water
Local alignment Global alignmentSimilarity Identity
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Pair wise Sequencing Alignment
Conclusion
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Pair wise Sequencing Alignment
Conclusion
??? ???INPUT
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
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Conclusion
LocalProcess Global
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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Conclusion
LocalProcess Global
Smith-Waterman algorithm
• Types of AlgorithmNeedleman-Wunsch
algorithm
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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Conclusion
LocalProcess Global
Smith-Waterman algorithm
• Types of Algorithm
• Types of software
Needleman-Wunsch algorithm
WATER NEEDLE- Parameters-
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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Conclusion
LocalProcess Global
Smith-Waterman algorithm
• Types of Algorithm
• Types of software
Needleman-Wunsch algorithm
WATER NEEDLE- Parameters-
E-DNA or BLOSUM or PAM E-DNA or BLOSUM or PAM• Types of Matrix
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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Conclusion
LocalProcess Global
Smith-Waterman algorithm
• Types of Algorithm
• Types of software
Needleman-Wunsch algorithm
WATER NEEDLE- Parameters-
E-DNA or BLOSUM or PAM E-DNA or BLOSUM or PAM• Types of Matrix
• GAP Penalties Default: Opening G – 10 Extension G – 0.5
Note: These settings can be customized accordingly!!!
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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Conclusion
INPUT
• Types of Algorithm
• Types of software
• Types of Matrix
• GAP Penalties
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Essence of Dynamic Programming
Conclusion
INPUT
• Types of Algorithm
• Types of software
• Types of Matrix
• GAP Penalties
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT Outcome 2
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT Outcome 2 Outcome 3
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Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT Outcome 2 Outcome 3 Outcome 4
Note: Do look out for Sequence Identity (%) , Similarity (%) and alignment of your input sequences