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