Non-uniqueProbe - Computational Molecular Biology Non-unique Probe Selection via Group Testing My T Thai [email protected] 2 My T Thai

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Computational Molecular Biology Non-unique Probe Selection via Group Testing
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My T. Thai [email protected] 2
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My T. Thai [email protected] 3
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My T. Thai [email protected] 4
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My T. Thai [email protected] 5 DNA Microarrays DNA Microarrays are small, solid supports onto which the sequences from thousands of different genes are immobilized, or attached, at fixed locations. Contain a very large number of genes in a small size chip. A tool for performing large numbers of DNA-RNA hybridization experiments in parallel.
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My T. Thai [email protected] 6 Applications Quantitative analysis of expression levels of individual genes The comparison of cell samples from different tissues. Computational diagnostics. Qualitative analysis of an unknown sample Identification of micro-bacterial organisms. Detection of contamination of biotechnological products. Identification of viral subtypes.
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My T. Thai [email protected] 7 Unique Probes vs. Non-unique Probes Unique probes Gene-specific probes or signature probes. Difficult to find such probes Non-unique probes Hybridize to more than one target. Difficult to design the test based on non-unique probes
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My T. Thai [email protected] 8 Probe-Target Matrix 12 probe candidates. 4 targets (genes). For target set S , define P ( S ) as set of probes reacting to any target in S. P ({1, 2}) = {1, 2, 3, 4, 7, 8, 9, 10, 12}. P ({2, 3}) = {1, 3, 4, 5, 6, 7, 8, 9, 12}. Symmetric set difference: P ({1, 2})∆ P ({2, 3}) = {2, 5, 6, 10}. Probes that separate two sets.
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My T. Thai [email protected] 9 Probe-Target Matrix Non-unique probe for each sequence group probe1(p1 ) probe2(p2 ) probe3(p3 ) s1 group 1 group 2 group 3 s2 s3 s4 s5 s6 s7 s8 s9 probe4(p4 ) probe5(p5 ) group1 group2 group3 t1 t2 t3 t4 t5 t6 t7 t8 t9 p1 1 1 0 0 0 1 0 0 0 p2 0 0 0 0 1 1 1 0 0 p3 1 0 1 0 0 0 0 1 0 p4 0 1 1 1 0 0 0 0 0 p3 0 0 0 0 0 0 1 1 1
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My T. Thai [email protected] 10 The Problem Given a sample with m items and a set of n non- unique proble Goal: determine the presence or absence of targets
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[email protected] 11 The Approach 3 Steps: Pre-select suitable probe candidates and compute the probe-target incidence matrix H . Select a minimal set of probes and compute a
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This note was uploaded on 05/20/2011 for the course CAP 5515 taught by Professor Ungor during the Spring '08 term at University of Florida.

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Non-uniqueProbe - Computational Molecular Biology Non-unique Probe Selection via Group Testing My T Thai [email protected] 2 My T Thai

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