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For an arbitrary dataset of twelve unrelated proteins that interact with AAA-domain proteins, for example, adding the default SLiMBuild equivalencies (AGS, ILMVF, FYW, FYH, KRH and DE) increased the runtime of TEIRESIAS by more than three orders of magnitude from 30 seconds to over 13 hours.
We observed that the combination of these two factors increased the runtime performance of the Flow-RM of 2-3 ofders of magnitude with respect to [ 2] approach.
Similar(58)
When M was decreased the accuracy went down, and when M was increased the runtimes went up without a corresponding increase in accuracy.
This modification results in more conformers but does not increase the runtime of the conformational sampling.
We would expect that a smaller value of δ would increase the runtime of our model.
The overlap check can reduce the number of final peak assignment possibilities, but will increase the runtime.
Allowing more mismatches increases the runtime superlinearly, because higher sensitivity requires shorter seeds with more chance occurrences.
Our results demonstrated that PEDI improved the consistency and the accuracy of parameter estimation while increasing the runtime efficiency.
Importantly, increasing α also increases the runtime of the algorithm significantly, such that one often needs to compromise on the sparsity of the network to keep computations feasible.
This feature enables scalability but, in this case, substantially increases the runtime as disk IO becomes the limiting factor for this small dataset (chromosome 22).
As expected, disabling the seed and allowing for indels near read termini improved the amount of high-quality hits recovered on the Helicos tSMS platform (+5.5%) while only slightly increasing the runtime cost.
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