Sentence examples for base composition at each from inspiring English sources

To determine the sequence variation along the 16S gene for the oral microbiome dataset, sequences were aligned using ClustalW [22], and variation in base composition at each position was computed in Mesquite [23].

Karlin and Mrazek [9], e.g., "predicted" whole-genome codon occurrences in humans on the basis of the within-codon ofcurrence of 12_, _23, and 1_3 dinucleotides and of the base composition at each codon position, quantities that obviously can be affected strongly by protein encoding and mRNA translatability (123 being a codon with its three positions labelled by the numbers 1, 2, and 3).

Note, incidentally, that i) expectations derived by assuming a single base composition per GC group, delivered very poor fit since a single base composition is not very suitable to fit the effects of amino-acid selection, and that ii) allowing a different base composition at each of the three codon positions delivers better fit but is biologically implausible.

Base compositions were determined for each genome segment (i.e., locus) analyzed and each unique base composition at each of these loci was assigned a letter according to decreasing number of occurrences (therefore, the letter A represents the most common allele identified at each locus).

Once the base composition at each codon position was calculated, the purine to pyrimidine ratio (R/Y) was calculated for each ORF of the dataset.

The chi-square test of homogeneity implemented in TREE-PUZZLE v5.2 [ 61] was used to evaluate variation in base composition at each codon position.

This dependence of codon usage on genome base composition (AT- or GC-richness) has been previously reported in several unicellular genomes.

Base composition, AT-skew and codon usage were calculated for the eight newly sequenced genomes and the 12 published Bombycidae mitochondrial genomes (Table  1).

The base compositions at each codon position are slightly biased: 54.4%, 61.8%, and 70.6% for the first to the third, respectively.

We did not use occurrence predictions that assume a different base composition at the 1st-, 2nd-, and 3rd-codon position, predictions that albeit attractive in terms of fitting potential are biologically absurd since they require a mechanism that lets DNA sequences mutate differently at the three codon positions.

Base composition at chromosome ends is significantly different from the coding core region.