To determine if the greater nucleotide diversity was due to an increase in the local mutation rate, we evaluated the nucleotide differences in the 28.5 kb sequenced region by comparing one human sequence with one chimpanzee sequence retrieved from the UCSC genome browser.
Techniques from experimental evolution could be useful in the context of tumor biology to systematically quantify mutation rates and evaluate costs of resistance (at least in vitro) and determine the role of the microenvironment in diversification.
We examined algorithm effectiveness across the mutation rate landscape by evaluating rates of 0.05, 0.04, 0.03, 0.02, 0.01, 0.008, 0.006, 0.004 and 0.002 for sample sizes of 500 and 1000 using a fixed number of generations (750) and a fixed population size (1000).
With respect to previously developed methods, ContrastRank evaluates the background mutation rate using the maximum value between the mutation rates of each gene in 1000 Genomes [ 79] and normal TCGA samples.
In a second step, we evaluated the mutation rate at microsatellite loci ranging from di- to hexanucleotide repeats, randomly chosen in the noncoding genome of P. pacificus.
They can be used to evaluate the mutation rate in chloroplast genomes and to detect sequences belonging to mitochondrial or nuclear DNA with a high similarity to the chloroplast genome (e.g. greater than 98%%) [19].
Direct estimates of mutation rate are also essential for evaluating theories of microsatellite evolution.
The 'frequentist' approaches evaluate the frequency of mutations in a gene compared with the background mutation rate (BMR), a measure of baseline probability of mutation for a given region of DNA [ 4- 6].
The mutation rate of MIRU-VNTR has been evaluated at 2.7 × 10 3/loci/year (3 ).
To adjust for any difference between ethnic groups, the association between LKB1 mutation rate and each characteristic was also evaluated as stratified contingency tables.
The parameters 150 and 50% were recommended by (Kumar and Cowen, 2010); we also evaluated a 10% mutation rate (a secondary peak according to their work) and performance was slightly worse (data available from the authors).
