Synthetic Sequence Synthetic Sequence Design for Signal Design for Signal Location Location Yaw-Ling Lin ( 林 林 林 ) Dept Computer Sci and Info Engineering College of Computing and Informatics Providence University, Taiwan E-mail: [email protected]http://www.cs.pu.edu.tw/~yawlin 111/06/17 Synthetic Design for Signal Location 1
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Synthetic Sequence Design for Signal Location Yaw-Ling Lin ( 林 耀 鈴 ) Dept Computer Sci and Info Engineering College of Computing and Informatics Providence.
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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
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.
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
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.
• 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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