The experimental results show a speedup factor of more than 14x over the Infernal−1.0 with QDB optimization for the alignment of a single long RNA sequence to a large CM model with thousands of states running on a PC platform with Intel Dual-core 2.5 GHz CPU.
The use of multiple genome indices and optimization of the alignment phase parameters (see below) is the basis of the enhanced detection of conserved sequences between evolutionarily distant orthologous DNAs.
Optimization of the alignment i.e removal of variable spacer region and alignment of C-terminal region was performed using GeneDoc [ 33] The Modelgenerator [ 34] was used to obtain the model and parameters for the likelihood analysis for the alignment of VerFtsZ and FtsZ.
In case of the reference (where no optimization in performed), the alignment of HOP setting, and thus of the performance, with the current network status happens much slower, after the changes have actually stopped.
Most of these publications on optimizing urban rail transit designs focused on the alignment optimization between two or more predetermined stations, whereas the selection of station locations may actually be even more challenging.
Note that the optimization of alignment is to minimize the total alignment score due to the negative signs in Eq. (1).
The results indicate that travel-time cost, which is often neglected by highway agencies in selecting alignments, significantly affects the alignment optimization.
Although several mathematical models have been developed to solve the alignment optimization problem, most of them emphasize either horizontal or vertical alignments, and only yield a suboptimal solution to the problem.
Finally, the results confirm that all dominating and alignment-sensitive costs should be simultaneously evaluated in the alignment optimization process because many trade-off opportunities exist among those costs.
Despite the optimization of alignment parameters, suboptimal or ectopic alignments occasionally occurred.
