Synthetic Sequence Design Synthetic Sequence Design for Signal Locationfor 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.twhttp://www.cs.pu.edu.tw/~yawlin

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OutlineOutline• Motivation• Introduction• Terminology Definition• Signal location search• Group testing designs• Adjacent levels of the Hasse diagram• Suggested Designations• Conclusion

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Synthetic BiologySynthetic Biology

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Synthetic BiologySynthetic Biology

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What have we done with synthesisWhat have we done with synthesis

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IntroductionIntroduction• 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.

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ContributionContribution

• 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.

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Biological Signal LocationBiological Signal Location

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Design criteria for sequence Design criteria for sequence signal searchsignal 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.

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A Simple Design and ChallengesA Simple Design and Challenges

• In the previous design, n = 16 and t = 4.

• Multiple Signals? Region Boundaries?

• Experimental Robustness?

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2-consecutive positive matrix2-consecutive positive matrix

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A cyclic 2-consecutive positive detectable matrix such that its column is a k-set (out of t elements) such that each two adjacent k-sets has distinct unions which are (k+1)-sets.

Middle Level ConjectureMiddle Level Conjecture

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Middle Level CoverageMiddle Level Coverage

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Adjacent Level LemmaAdjacent Level Lemma

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Cycles crossing adjacent levelsCycles crossing adjacent levels

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Shimada and Amano (2011), running time about 81 days:

Consecutive Positives Detectable MatrixConsecutive Positives Detectable Matrix

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Main result: Main result: Non-adpative Group TestingNon-adpative Group Testing

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Designing Consecutive Positives Detectable MatrixDesigning Consecutive Positives Detectable Matrix

Experiment ResultsExperiment Results

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Consecutive Positives Detectable MatrixConsecutive Positives Detectable Matrix

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Design EfficiencyDesign Efficiency

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• 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.

ConclusionConclusion• 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.112/04/19 Synthetic Design for Signal Location 22

Conclusion Conclusion (Theory)(Theory)

• Equivalence of middle level conjecture to the adjacent level conjecture.

• Improvement of the consecutive positive matrix design.

• Future and continuous works:o More than one consecutive positives.o Efficient algorithms for false reads.o TagSNP selection in the haplotype block.o Further experiments on related biomedical

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Thank You!

Any Question?

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Thank you.

Q&A

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What Weekday is Today?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

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