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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: [email protected]://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.112/04/21 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
haplotype data.112/04/21 Synthetic Design for Signal Location 23
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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