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PSA [Conclusion]

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Sam Tan

LSM2241 - Pairwise Sequencing Alignment Presentation's Conclusion

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CONCLUSION- Take home message - Matrix Gap opening Gap extension Dynamic Programming Needle Water Local alignment Global alignment Similarity Identity
Conclusion Pair wise Sequencing Alignment
Conclusion Pair wise Sequencing Alignment ??? ??? INPUT
Conclusion Pair wise Sequencing Alignment DNA Protein INPUT Types of Alignment Local Global Local Global
Conclusion Pair wise Sequencing Alignment DNA Protein INPUT Types of Alignment Local Global Local Global
Conclusion Pair wise Sequencing Alignment DNA Protein INPUT Types of Alignment Local Global Local Global Local Global Process
Conclusion Pair wise Sequencing Alignment DNA Protein INPUT Types of Alignment Local Global Local Global Local Global Process Smith-Waterman algorithm Needleman-Wunsch algorithm ,[object Object],[object Object]
Types of softwareWATER NEEDLE - Parameters-
Conclusion Pair wise Sequencing Alignment DNA Protein INPUT Types of Alignment Local Global Local Global Local Global Process Smith-Waterman algorithm Needleman-Wunsch algorithm ,[object Object]
Types of softwareWATER NEEDLE - Parameters- E-DNA or BLOSUM or PAM E-DNA or BLOSUM or PAM ,[object Object],[object Object]
Types of softwareWATER NEEDLE - Parameters- E-DNA or BLOSUM or PAM E-DNA or BLOSUM or PAM ,[object Object],Default: Opening G – 10 Extension G – 0.5 Note: These settings can be customized accordingly!!! ,[object Object],[object Object]
Types of software
Types of Matrix
GAP Penalties,[object Object]
Types of software
Types of Matrix

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PSA [Conclusion]

  • 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.
  • 8. Types of softwareWATER NEEDLE - Parameters-
  • 9.
  • 10.
  • 11.
  • 12. Types of software
  • 13. Types of Matrix
  • 14.
  • 15. Types of software
  • 16. Types of Matrix
  • 17.
  • 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