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Regarding the methodological contribution of the manuscript, it lacks several desired/required characteristics of a methods paper, such as statistical formalism and background information, benchmarking with other methods and simulations with randomized datasets.
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These measures are important, as they facilitate benchmarking with other institutions running similar courses.
At the same time, the author goes into great detail to highlight the agreement with previous biochemical and structural studies which make this part of the description of the used dataset valuable as benchmark for comparison with other methods.
The Markov model may also be used as a benchmark to make comparison with other methods.
Below we benchmark the performance of PHLAT together with other methods using multiple public and in-house datasets.
We benchmarked KalignP using gap penalties from predicted secondary structure with other methods on Balibase 3.0.
With a view to design a well intelligent system that can effectively correlate multiple monitored variables with corresponding defect types, a novel intelligent fault diagnosis method with multivariable ensemble-based incremental support vector machine (MEISVM) is proposed, which is testified on a benchmark of roller bearing experiment in comparison with other methods.
To compare the runtime of our approach with other methods, we used two benchmark sets: a set of 50 simulated DNA sequences of 16 000 nt each and our test set of 14 plant genomes.
Compared with other methods, Soxhlet is something of a benchmark technique as few parameters can affect the extraction.
The restriction to protein-coding regions and the limited availability as a web server makes a comparison with other methods difficult for a genome-wide benchmark.
In order to compare performance of meta-analysis with other methods for identifying TF targets, we prepared a benchmark dataset of TF-target pairs in Arabidopsis, which were obtained from the AGRIS database and AtRegNet [ 34].
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