Sentence examples for mutation matrices from inspiring English sources

We also derive mechanistic template mutation matrices (MTMMs) representing estimated mutation patterns putatively emanating from the four mutational mechanisms studied here: oxidative damage, UV-induced damage involving CPD formation, deamination of 5mCpG, and the action of members of the APOBEC family of cytosine deamination enzymes.

Similarly, no straightforward prediction seems possible when the evaluated sequences have, e.g., a GC that is very different from the equilibrium GC that the evaluated mutation matrices generate.

For instance, we have observed that the relative 64×4 mutabilities are mostly much higher than 100% when they are estimated using coding regions whose GC matches the actual GC of the alignments from which the substitutions used to estimate mutation matrices were retrieved, rather than the equilibrium GC generated by the estimated matrices.

We evaluated and contrasted the mutability under 64×4 and 4×4 mutation of those coding regions in our largest human dataset whose GC123 matches the equilibrium GC123 generated under Granthamian amino-acid selection by the 64×4 and 4×4 mutation matrices derived from intronic and coding-region DNA (a GC content that is very similar for each pair of matched 64×4 and 4×4 matrices; see above).

The mutation matrices were prepared using the same procedure described in [ 11].

In addition, mutation matrices were also inferred using the method of Nielsen et al. (2007) for both Arabidopsis species.

For example, when a network area with enriched number of mutated genes is located, the corresponding mutation matrix can be retrieved to investigate mutation status for these genes in individual samples.

The observed overlap of mutated samples for a pair of genes in the original binary mutation matrix was compared with the overlap values derived from the 10,000 permuted matrices.

In particular, using the eigenvectors of the mutation matrix as the new basis, we show that the quasispecies distribution approaches a binomial one and give simple estimates for the speed of convergence.

Using the fact that the mutation matrix in the case of a permutation invariant fitness landscape has a special tridiagonal form, a change of the basis is suggested such that in the new coordinates a number of analytical results can be obtained.

One of the first of such models was the PAM (point accepted mutation) matrix [4].