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(c) Mutation position and frequency in each replicate (red bar, isolate 1; green bar, isolate 2; blue bar, isolate 3).
Hutter, S. et al. No correlation between NF1 mutation position and risk of optic pathway glioma in 77 unrelated NF1 patients.
Given existing information regarding mutation position and risk of cognitive disability the subset of 58 DMD cases was re-analysed with Dp140utr cases reclassified as primary affecting Dp427 and Dp260 isoforms (Table 2 model 14, and Figure 2).
Table 1 shows the Mutation Surveyor® report indicating the mutation position and score.
The symbol is constructed with sequence accession number in GenBank, sequence type symbol, mutation position and sequence change.
For the interacting pairs, we found 207 non-synonymous SNPs without overlap with a correlated mutation position, and 19 with overlap with a correlated mutation position.
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Overall, there are large differences between different interacting protein pairs with respect to the number of correlated mutation positions and motifs that coincide.
The RefSeq sequence was used to calculate position frequency matrices, detection of new mutation positions, and to estimate distances from RefSeq to the FLIC and RefSeq to new mutants we planned on introducing into the FLIC.
The identified 1205 new mutation positions and the older dataset of genomic sequences (2012.02.12) were submitted to the GeneSV system to test its efficacy in predicting novel viable mutations and to measure the robustness of the system by assessing the impact of these newly discovered mutations on the predictions already made.
Comparison with randomly generated position pairs (see Methods) showed that the F-score (harmonic mean of coverage of correlated mutation positions and of predicted interaction motifs, 0.46 for the interacting pairs and 0.37 for the non-interacting pairs) was significantly different from random for the interacting protein pairs (p < 0.001), but not for the non-interacting protein pairs (p~0.5).
We trained the classifiers on this data (consisting of 1015 true somatic mutations and 2354 non-somatic mutation positions) and conducted a rigorous evaluation of these methods using a cross-validation framework and hold-out test NGS data from both exome capture and whole genome shotgun platforms.
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