1. Selecting Restriction Enzymes for Terminal Restriction Fragment Length Polymorphism based on Phylogenetic Distance Present: Mei, Ko-Jen N18981246 機械博二

2. Outline Introduction Algorithm – Skeleton – Distinct Matrix Establishment for Clusters – Distinct Matrix Establishment for Sample Vector of Restriction Enzymes – Match and Weight Program Application Discussion Conclusion

3. Introduction What is T-RFLP? What is phylogenetic distance matrix? What is restriction enzyme? What is the concern of selecting restriction enzymes for T-RFLP? How to solve this problem in the past?

4. Algorithm - Skeleton

5. Algorithm - Distinct Matrix Establishment for Clusters

6. Algorithm -Distinct Matrix Establishment for Sample Vector of Restriction Enzymes (I)

7. Algorithm -Distinct Matrix Establishment for Sample Vector of Restriction Enzymes (II)

8. Algorithm- Match and Weight (I) Artificial WeightNatural Weight Restriction Enzyme\ClusterSAMEDIFFERENT SAMEWeight0 DIFFERENT01

9. Algorithm- Match and Weight (II)

10. Program Application

11. Discussion (I) mask Find the best mask for a target vector from several candidate vectors Why natural weight meaningful for identical element? – Difference between classes higher then difference within class – (Cluster, Restriction Enzyme) = (SAME, SAME) does not influence the result significantly – The distinctibility is remained

12. Discussion (II) How artificial weight matrix defined? – Distinctibility for species (Cluster, Restriction Enzyme) = (DIFFERENT, DIFFERENT) (Cluster, Restriction Enzyme) = (DIFFERENT, SAME) – Distinctibility for clusters (Cluster, Restriction Enzyme) = (DIFFERENT, DIFFERENT) – Identity within cluster (Cluster, Restriction Enzyme) = (SAME SAME) Not so important; weight it! Since the importance lower than distinctibility, the weight value is usually within 0~1. Restriction Enzyme\ClusterSAMEDIFFERENT SAMEWeight0 DIFFERENT01

13. Conclusion Choosing the most identical vector – from a set of sample vectors – to match the given clusters applied for choosing restriction enzymes – according to the clusters clusters can be achieved – by User-defined – by phylogenetic distance matrix weighting can be achieved – according to phylogenetic distance matrix – according to artificial weight. The application can provide an easy environment to manipulate clusters and selecting method.