Sentences with phrase «positions of the codon»

These coding regions of the genome have a characteristic broad distribution of GC3 (fraction of cytosine and guanine in the third position of a codon) with over half the GC3 - rich genes (GC3.

Not exact matches

Reducing this variation by RY recoding of purines (R) and pyrimidines (Y) on the third codon position (SM4) made the c123 tree topology more similar to the c12 topology (Fig. 2 and fig.

The differences between coding versus noncoding trees were not solely due to shorter sequence length of the coding data, because the full coding data set (13.3 million bp for c123) produced a tree with fully supported (100 % BS) relationships that were incongruent with those fully supported in the intron (19.3 million bp), TENT (37.4 million bp without the third codon position), and WGT (322.1 million bp)(Figs. 2 and 5B, and table S3).

Trees created from analysis of the first and second codon positions (exon c12) of the TENT data also had lower levels of BS (~ 39 to 64 %) but with more topological differences on the deep branches (Figs. 2, 4C, and 5A), yet all but one of the fully resolved relationships (local difference in egret + ibis + pelican) were congruent with the TENT (Fig. 5B).

We further investigated the source of the conflict in the protein - coding genes (SM11) and found that trees using all codon positions from the 10 % most compositionally homogeneous (low - variance) exons (n = 830) were most congruent with the c12 tree and, thus, more similar to the TENT than to the c123 tree (Figs. 2 and 6A; cladograms in fig.

To estimate the avian timetree with genomic - scale data, we used first and second codon positions from 1156 clock - like exon genes (which do not strongly exhibit the above protein - coding compositional bias), calibrated with 19 conservatively chosen avian fossils (plus nonavian outgroups) as minimum bounds for lineage ages (with a maximum - bound age constraint of 99.6 Ma for Neornithes), in a Bayesian autocorrelated relaxed clock method using MCMCTREE (77) on the fixed ExaML TENT topology (SM12).

(A) Cladogram of ExaML TENT avian species tree, annotated for nodes from Fig. 2 (letters), for branches with less than 100 % BS without and with (parentheses) third codon positions, for strong (> 75 % BS) intron gene tree incongruence and congruence, and for indel congruence on all branches (except the root).

An ExaML TENT tree that included the third codon position (TENT + c3) was identical in topology to the ExaML TENT without the third codon position and had increased support for six of the nine branches that had less than 100 % BS (fig.

Phylogenetic inference was carried out using a partitioned (codon positions 1 — 2 and 3) supermatrix of 20,384 protein - coding genes from Ensembl v72 (80) following quality filtering, using the longest transcript for each gene.

Identification of significant phylogenetically informative sites at the nucleotide level revealed positions not only contributing to clade differentiation, but which are located at or proximal to codons associated with resistance to protease inhibitors (NS3 Q41) or polymerase inhibitors (NS5B S368).

Now, place your right finger over the third position codon (G) in the same row of the last column (G).

First, place your left finger on the first position codon (A), in the first column of the table.