Sentence examples for molecular substitution using from inspiring English sources

Data collection statistics are reported in Table 2. Structures were determined by molecular substitution using previously solved structures (PDBs 1u7d for the apo-open structure and 2zp1 with substrate omitted for the apo-closed and substrate-bound structures).

Alignments of these data and a published complete sequence from Tursiops truncatus with primate MCPH1 were utilized in phylogenetic analyses and to estimate ω (rate of nonsynonymous substitution/rate of synonymous substitution) using site and branch models of molecular evolution.

Phylogenies were reconstructed both by the neighbor joining method under default settings of amino acid substitution using PAUP* version 4.0b10 software [54] and by Bayesian inference under the Hasegawa, Kishino, Yano nucleotide substitution model [55] and a relaxed molecular clock [56] using BEAST 1.4 software.

erythropoietin substitution using epoetin theta.

Predicting the Functional, Molecular and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models.

For choosing the molecular substitution model we analysed the data using MrModelTest v2 [ 98], and based on the Akaike Information Criterion, the most parameter-rich model GTR+G+I was suggested.

As previously, analyses were performed using a lognormal-relaxed molecular clock using a substitution rate (ucld. mean) following a normal prior distribution of mean 0.01973 [ 33] and a standard deviation of 0.005 to take into account some rate uncertainty.

Influenza B virus data sets were also simulated under a strict molecular clock using divergence times, substitution rates and other substitution parameters estimated by Physher.

The molecular substitution models were evaluated with ModelTest [ 67] to select the preferred model among those that could be used in *BEAST, separately for each locus.

Bayesian analyses were performed in BEAST v1.4.7 [ 66] assuming an uncorrelated lognormal relaxed molecular clock model using the substitution and site heterogeneity models determined by ProtTest and with a Yule process speciation tree prior.

More generally, our combined genomic/phenotypic approach was used to show where molecular substitutions tended to cluster in the genomes of phage ϕ6 populations subjected to the host-use challenges.