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3 Radioisotopically labeled OAADPrs were used to determine KIEs by the competitive method.
The kinetic isotope effects were determined using the competitive method in which isotope ratios of the OAADPr substrate were measured by mass spectrometry before and after depletion by the MacroD1 catalyzed reaction.
As we mentioned above, both GenGen and ALIGATOR belong to the "competitive" method group, while the Plink set-based test and SRT belong to the "self-contained" group [ 7, 8].
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The competitive methods, i.e., LPA-ICI and bilateral filtering, should not be, however, discarded as fast implementations of those do exist as well.
The self-contained approaches are more powerful for testing the H0SC hypothesis and allow for subject-level sampling or permutation methods for estimating the empirical null distribution of the test statistic, while the competitive methods do not [1].
Furthermore, MNet, unlike the competitive methods, enables an easy selection of suitable parameters.
We use the best value for parameters obtained by cross-validation for all the competitive methods.
Especially, for complexes with multiple binding sites our approach is able to outperform the competitive methods.
In overall, the results demonstrate that our method predicts RNA-RNA interactions more accurately in compare to the competitive methods.
In particular, we train all the competitive methods using all the available OMIM data collected until August 2011.
Furthermore, our method was compared with the DP-based algorithms including NUPACK (Dirks and Pierce, 2003 20044) and PKNOTS (Rivas and Eddy, 1999), as well as the competitive methods used in the previous experiment.
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