While the C3H strain was used for mutation mapping, the 129S1 strain was used for the majority of results and figures presented here.
For visualization and comparison of general residue positions, such as for mutation mapping, we necessarily used homology models to account for the changes in the respective sequences of each strain to be compared.
RFLP (Restriction fragment length polymorphism) and AFLP (Amplified fragment length polymorphism) markers have been developed and used for generating genetic linkage maps and for mutation mapping, map-based cloning, and genome synteny comparisons [ 4, 20- 23].
In theory, low thresholds should be used for mutation mapping, increasing the number of false positives but reducing the number of false negatives.
Samples of venous blood were collected (with EDTA) from 18 affected and 41 unaffected animals for mutation mapping and frequency analysis.
While ranking the epitopes for mutation mapping, epitopes with calculated IC50 values/scores above 100 were not included since such peptide-epitopes were unlikely to yield significant immunogenicity.
Altogether we identified ~31,300 polymorphisms (23,800 SNPs and 7,500 medium and small indels) between AF16 and HK104 that promise to be a valuable resource for mutation mapping and genome evolution studies.
The higher false positive rate at mutant sites covered 3X 5X in the PB306, HK104, and PB800 MA lines (compared with N2) is most likely related to the fact that the reference genome sequence required for mutation mapping differed from strains used as MA line progenitors.
High-resolution mutation mapping reveals parallel experimental evolution in yeast.
