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They reflect these two properties using a mutation matrix and a scoring function.
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After DNA alteration, the student can determine the type of phenotype change caused by the mutation using a "mutation table".
After processing these data, we established two matrices, that is, a mutation matrix and an expression matrix, which cover 90 samples and 1126 genes.
Step 1: A mutation matrix is obtained by combining somatic mutations and CNVs, and an expression matrix is generated from gene expression profiles.
Below is a mutation matrix for three traits (t1, t2 and t3).
Pairwise distances between sequences, for comparing evolution of AlkB domains to other viral domains, were computed directly from ClustalX alignments with local tools, using the Blosum50 mutation matrix [ 47], but without any correction for multiple substitutions.
Using the mutation matrices given in Singh et al. (2007), we adjusted the ancestral GC content (and thus the denominator of the rate calculation) for both D. melanogaster and D. sechellia by multiplying the number of ancestral G's, C's, A's, and T's by the values given in supplementary table 1 (Supplementary material online).
We simulated random mutations by using a compositional substitution matrix based on the nucleotide frequencies of the original (wild type) genome [ 47].
Calculation of synonymous and non-synonymous positions was undertaken for each P. falciparum ortholog using a standard substitution matrix (assuming equal mutation rates) with Jukes-Cantor correction [ 49].
"It's just using a different matrix".
Multicollinearity was assessed using a correlation matrix.
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