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By contrast, the mutation dataset used in our independent benchmark was collected from the SwissVar [Mottaz et al., 2010] portal.
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> -wrap-foot> As our prediction threshold was derived using the same mutation datasets used in this benchmark (albeit using a leave-one-out analysis), and a large proportion of driver mutations is also present in our training data, we recognize the potential for bias in the observed performances.
In any fair comparison, care should be taken to reduce the potential overlap between the mutation datasets used for training and testing; however, this level of testing is not possible, as it would require obtaining and retraining each algorithm with common datasets.
The final dataset used for analysis included 408 activating, 1932 neutral, and 9736 deleterious mutations.
We also describe in the Supplementary Material a dataset used to assess the ability of mCSM in predicting disease-related mutations.
If so, the dataset used by the study could be flawed.
Although this agreement between the lymphoblastoid chromatin dataset used in this analysis and other more general datasets is reassuring, GC content has previously been associated with rates of mutation and selection.
Since the dataset used for the MAL8 is publicly available and continues to grow, obtaining sufficient data for additional STRs may enable estimation of their mutation rates.
To directly test whether synonymous sites of mammalian rhodopsins are under selection, we analyzed the coding sequences of our rhodopsin dataset using the mutation-selection models [ 32] in PAML 4.7 [ 67].
To understand the relationship between tumor types and number of mtDNA mutations, Poisson regression and ANOVA were applied to our dataset using R software (http://www.r-project.org).org
The ability of the BANN-trained classifier to distinguish between BRCA1/2 mutation carriers and non-carriers was evaluated in the testing dataset using several approaches.
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