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The best chromatographic peak model for fitting the XIC constructed by DBSCAN is EMGM with a fitting score R of 0.9937, while the XIC constructed by the variation window approach does not have a complete peak shape and therefore can only detecte three peaks and misses the far left hidden peak at retention time of 441 s (the fitted peak 3 in Figure 6C).
RAId_DbS integrates the theoretical pdf, obtained from fitting score histogram with Eq. (17), from the high-scoring end down in order to obtain the P-value P(S) for score S. The E-value for a peptide with score S is then obtained by multiplying the P(S) by the effective database size.
This is further supported by fitting scores from Chimera (Pettersen et al., 2004): the conserved part has a fitting score of 43.1, much higher than 16.7: that of non-conserved part.
This is also supported by fitting scores from Chimera (Pettersen et al., 2004): the conserved part has a fitting score of 0.80, much higher than 0.49: that of non-conserved part.
The best fitting score for a particular model was then used for comparison to other models.
The simulation results are given in the form of fitting score and variation frequency of each pattern of 48 genotypes.
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The best fitting model for each peak is then determined based on fitting scores, that is, the maximum R value.
For each model, we continued this process of parameter set selection and parameter range narrowing until the fitting scores no longer improved.
Even though the EMGM model performed the best, the difference among the fitting scores of these five models is quite small.
From the simulation results, we draw the following conclusions: (1) Rule I gives more genotypes (RowID) with high fitting scores nearly 100% than Rule II to cover predicted patterns of three simulation targets.
(iii) For lin-15; lin-12ko double mutants (RowID 21), the fitting scores in the results of ST and STA drop to a quite low value below 15% by using either Rule I or Rule II.
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Justyna Jupowicz-Kozak
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