Massively parallel algorithm for multiple biological sequences alignment

Author(s):  
Plamenka Borovska ◽  
Veska Gancheva ◽  
Nikolay Landzhev
Author(s):  
Jorg Keller ◽  
Gabriele Spenger ◽  
Steffen Wendzel

We present and motivate a parallel algorithm to compute promising candidate states for modifying the state space of a pseudo-random number generator in order to increase its cycle length. This is important for generators in low-power devices where increase of state space to achieve longer cycles is not an alternative. The runtime of the parallel algorithm is improved by an analogy to ant colony behavior: if two paths meet, the resulting path is followed at accelerated speed just as ants tend to reinforce paths that have been used by other ants. We evaluate our algorithm with simulations and demonstrate high parallel efficiency that makes the algorithm well-suited even for massively parallel systems like GPUs. Furthermore, the accelerated path variant of the algorithm achieves a runtime improvement of up to 4% over the straightforward implementation.1  


2009 ◽  
Vol 16A (6) ◽  
pp. 411-418 ◽  
Author(s):  
Luong Van Huynh ◽  
Cheol-Hong Kim ◽  
Jong-Myon Kim

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