psa [conclusion]
DESCRIPTION
LSM2241 - Pairwise Sequencing Alignment Presentation's ConclusionTRANSCRIPT
CONCLUSION- Take home message -
Matrix Gap opening Gap extension Dynamic Programming Needle Water
Local alignment Global alignmentSimilarity Identity
Pair wise Sequencing Alignment
Conclusion
Pair wise Sequencing Alignment
Conclusion
??? ???INPUT
Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Conclusion
LocalProcess Global
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
Conclusion
LocalProcess Global
Smith-Waterman algorithm
• Types of AlgorithmNeedleman-Wunsch
algorithm
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
Pair wise Sequencing Alignment
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
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
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
Conclusion
INPUT
• Types of Algorithm
• Types of software
• Types of Matrix
• GAP Penalties
Essence of Dynamic Programming
Conclusion
INPUT
• Types of Algorithm
• Types of software
• Types of Matrix
• GAP Penalties
Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT
Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT Outcome 2
Pair wise Sequencing Alignment
Conclusion
DNA ProteinINPUT
LocalTypes of Alignment
Global Local Global
PROCESS
Outcome 1OUTPUT Outcome 2 Outcome 3
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