To accelerate the alignment selection, our aligner employs fine-grained parallelism from Single instruction, Multiple data (SIMD) vector execution units with the use of SSE2 assembler instructions.
BWA-SW [30], an implementation of the Burrows-Wheeler aligner combined with a Smith-Waterman search uses heuristics to accelerate the alignment process.
Although not used in this study, the mothur implementation enables users to use multiple processors to accelerate the alignment.
Second, it accelerates the alignment step.
Given this requirement, we can design spaced seed templates (Ma et al., 2002) spanning the entire read (Jiang and Wong, 2008; Lin et al., 2008; Smith et al., 2008), or quickly filter out poor matches, for example, by applying q-gram filtration (Rumble et al., 2009; Weese et al., 2009) or by bounding the search process (Li and Durbin, 2009), and thus accelerate the alignment.
But if Mr. Clinton managed some important centrist achievements — including a crime bill, the passage of Nafta and welfare reform — he also personally became (especially in the wake of the Monica Lewinsky scandal) a flash point for controversy, which "accelerated the trend toward a political alignment that divided the nation more along lines of culture than class".
Globalisation accelerated the branding process.
Epilepsy accelerated the process.
The idea of our proposed method can be applied to CUDASW++ 3.0 in the future to accelerate the processing of alignments with short query sequences for the intertask kernel.
Thus, the proposed combination will result in an accelerated RNA alignment approach compared to the underlying RNA alignment approach alone, which will work for any available alignment method.
