Synthetic Sequence Design for Signal Location

1. Synthetic Sequence Design for Signal Location Yaw-Ling Lin ( 林 耀 鈴 ) Dept Computer Sci and Info Engineering College of Computing and Informatics Providence University, Taiwan E-mail: yllin@pu.edu.tw http://www.cs.pu.edu.tw/~yawlin Synthetic Design for Signal Location

2. Outline Motivation Introduction Terminology Definition Signal location search Group testing designs Adjacent levels of the Hasse diagram Suggested Designations Conclusion Synthetic Design for Signal Location

3. Synthetic Biology Synthetic Design for Signal Location

4. Synthetic Biology Synthetic Design for Signal Location

5. What have we done with synthesis Synthetic Design for Signal Location

6. Introduction Large-scale synthesis opens new doors for rapid signal detection: Replace a wild type gene coding sequence (W) with a different but synonymous encoding (D). If the phenotype changes (e.g., the organism dies), it implies that there must be a critical signal at some location within that region. Synthetic Design for Signal Location

7. Contribution • A Group-Testing Approach for Biological Signal Location. • Group Testing for Expensive Pools. • Improved Designs for Consecutive Positive Group Testing. • Middle-Levels Conjecture Equivalence. • Web link: http://www.algorithm.cs.sunysb.edu/signalSearch. Synthetic Design for Signal Location

8. Biological Signal Location Synthetic Design for Signal Location

9. Design criteria for sequence signal search • Experiences with polio and adenovirus. • To construct t tests (design sequences) capable of pinpointing the location of a signal of length at most m (~20 to 60) bases as tightly as possible in a region of length g (~2k nt). • We aim to partition the region into n segments and construct t tests to determine which segment contains the critical signal. Synthetic Design for Signal Location

10. A Simple Design and Challenges • In the previous design, n = 16 and t = 4. • Multiple Signals? Region Boundaries? • Experimental Robustness? Synthetic Design for Signal Location

11. 2-consecutive positive matrix A cyclic 2-consecutive positive detectable matrix such that its column is a k-set (out of telements) such that each two adjacent k-sets has distinct unions which are (k+1)-sets. Synthetic Design for Signal Location

12. Middle Level Conjecture Synthetic Design for Signal Location

13. Middle Level Coverage Synthetic Design for Signal Location

14. Adjacent Level Lemma Synthetic Design for Signal Location

15. Cycles crossing adjacent levels Shimada and Amano (2011), running time about 81 days: Synthetic Design for Signal Location

16. Consecutive Positives Detectable Matrix Synthetic Design for Signal Location

17. Main result: Non-adpative Group Testing Synthetic Design for Signal Location

18. Designing Consecutive Positives Detectable Matrix Synthetic Design for Signal Location

19. Experiment Results Synthetic Design for Signal Location

20. Consecutive Positives Detectable Matrix Synthetic Design for Signal Location

21. Design Efficiency • Our design: • Colbourn’s design (1999): • In particular, for r=3, d=3, Colbourn’s design create an 10 x 16 matrix; while our design, M3(7,3) gives a 10 x 105 matrix. Synthetic Design for Signal Location

22. Conclusion We give a new class of consecutive positive group testing designs, which offer a better tradeoff of cost, resolution, and robustness than previous designs for signal search. Let n be the number of distinct regions, and d the number of consecutive positives regions. The design identifies the positive regions using t tests, where Given the target sequence, we propose one/two-round designs to maximize the number of inspected items n (therefore minimized boundary resolution). Future works: faults-detecting decoding algorithms. Synthetic Design for Signal Location

23. Conclusion (Theory) Equivalence of middle level conjecture to the adjacent level conjecture. Improvement of the consecutive positive matrix design. Future and continuous works: More than one consecutive positives. Efficient algorithms for false reads. TagSNP selection in the haplotype block. Further experiments on related biomedical haplotype data. Synthetic Design for Signal Location

24. Thank You! Any Question? Synthetic Design for Signal Location

25. Synthetic Design for Signal Location

26. Thank you. Q&A Synthetic Design for Signal Location

27. What Weekday is Today? • Magic Number: • - 4/4, 6/6, 8/8, 10/10, 12/12 • - 7/11, 9/5 [also 11/7, 5/9] • - 3/0? [implying 2/28, 2/0 = 1/31] • Extension: • - 365 = 52 * 7 + 1 • - Leap Year? • 2012:3; 2013:4; 2014:5; 2015:6; 2016:1 • 20yy: [5yy/4]+2 mod 7 Synthetic Design for Signal Location