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

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

3. Comparison between approximate O(N 2 ) alignment and O(N 3 ) alignment produced by DINAMelt Server* *Markham and Zuker (2005) Nucleic Acids Research, 33, W577-W581 Temperature [ºC]  Tm [ºC]  G [kcal mol -1 ] ~ 0.7 kcal mol -1 ~ 1.9 ºC

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

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

6. T 1000 >>Q 100 >>W 10 Q 1000 >>T 100 >>W 10 Q 1000 >>W 100 >>T 10 W 200 >Q 100 >>T 10 T 1000 >>W 100 >>Q 10 W 200 >>T 100 >>Q 10