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Improved Assay-dependent Searching of Nucleic Acid Sequence Databases

Improved Assay-dependent Searching of Nucleic Acid Sequence Databases. Jason Gans Los Alamos National Laboratory. O(N 2 ) Thermodynamic alignment.

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Improved Assay-dependent Searching of Nucleic Acid Sequence Databases

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  1. Improved Assay-dependent Searching of Nucleic Acid Sequence Databases Jason Gans Los Alamos National Laboratory

  2. O(N2) Thermodynamic alignment Define a “reduced” pair-wise free energy function, whose exact O(N2) minimum energy alignment approximates the minimum energy alignment of the near neighbor free energy function, Determine free parameters by simulated annealing-based minimization of evaluated at the alignments produced by Aligned bases Gap regions Temperature

  3. Comparison between approximate O(N2) alignment and O(N3) alignment produced by DINAMelt Server* DDG [kcal mol-1] ~ 0.7 kcal mol-1 ~ 1.9 ºC DTm [ºC] Temperature [ºC] *Markham and Zuker (2005) Nucleic Acids Research, 33, W577-W581

  4. Identification of STS primer binding sites in the human genome (DG match criteria)

  5. ThermonucleotideBLAST implements target splitting and adaptive segmentation Target segmentation Target & query segmentation t = # targets q = # queries w = # workers S/H = time to search one query Cost of target and query segmentation per worker Cost of target segmentation per worker time to load and hash one target

  6. T1000>>Q100>>W10 T1000>>W100>>Q10 Q1000>>T100>>W10 Q1000>>W100>>T10 W200>Q100>>T10 W200>>T100>>Q10

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