Sentence examples for empirical matrices from inspiring English sources

Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated.

Much like other empirical matrices, the HIV models assigned higher rates to those pairs that are separated by a single nucleotide substitution (see also Figure 2).

Because HIV sequences almost certainly do not have the same amino acid frequencies as those built into prior empirical matrices, the inclusion of HIV specific residue frequencies can be expected to improve the models.

A possible component of poor fit shown by existing empirical matrices on HIV sequences is the assumption that the sequences being compared have the same average amino acid composition as that used in producing the model.

We believe that with readily accessible modern computing power, it is now feasible to estimate and use organism specific empirical matrices for protein sequence analysis using powerful statistical techniques.

We first tabulated substitution rates inferred from the between-patient training set (HIV-Bm model) and from the within-patient training set (HIV-Wm model) and generated a graphical representation of six popular empirical matrices along with our two HIV specific matrices (Figure 1).

The 2D histogram can be seen as an matrix, which is called a gray subordinate matrix or empirical matrix (EM).

In practice, we sample 1,000 times the empirical data and compare each sampled empirical matrix of one household to the corresponding synthetic matrix, whose generation process cannot be randomized, obtaining one value of the (R_{0}) ratio from each comparison.

This allowed the use of a 6 × 6 general time-reversible rate matrix with free parameters rather than a fixed empirical matrix.

This test was based on the comparison of trees obtained with 2 non-nested models, "LG" and "CAT", using the "LG" empirical matrix.

Yet, in contrast to Sippl's approach, our metric [Single sTRucture Induced Evaluation (STRIKE)] relies on a purely empirical matrix, whose estimation does not involve any Boltzmann modeling.