We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonst...

Mutual correlation between segments of DNA or protein sequences can be detected by Smith-Waterman local alignments. We present a statistical analysis of alignment of such sequences, based on a recent scaling theory. A new fidelity measure is introduced and shown to capture the significance of the local alignment, i.e., the extent to which the correlated subsequences are correctly identified. It...

Extending the single optimized spaced seed of PatternHunter to multiple ones, PatternHunter II simultaneously remedies the lack of sensitivity of Blastn and the lack of speed of Smith-Waterman, for homology search. At Blastn speed, PatternHunter II approaches Smith-Waterman sensitivity, bringing homology search technology back to a full circle.

We have compared commonly used sequence comparison algorithms, scoring matrices, and gap penalties using a method that identifies statistically significant differences in performance. Search sensitivity with either the Smith-Waterman algorithm or FASTA is significantly improved by using modern scoring matrices, such as BLOSUM45-55, and optimized gap penalties instead of the conventional PAM250 ...

Gene sequencing problems are one of the predominant issues for researchers to come up with an optimized system model that could facilitate the optimum processing and efficiency without introducing overheads in terms of memory and time. This research is oriented towards developing such kind of system while taking into consideration of the dynamic programming approach called a Smith Waterman algo...

Propagation of P and SV waves in an elastic solid containing randomly distributed inclusions in a half-space is investigated. The approach is based on a multiple scattering analysis similar to the one proposed by Fikioris and Waterman for scalar waves. The characteristic equation, the solution of which yields the effective wave numbers of coherent elastic waves, is obtained in an explicit form ...

A novel experiment is used to show that the effect of a policy on the level of cooperation is greater when it is chosen democratically by the subjects than when it is exogenously imposed. In contrast to the previous literature, our experimental design allows us to control for selection effects (e.g. those who choose the policy may be affected differently by it). Our finding implies that democra...