Sentence examples for base composition codon usage from inspiring English sources

Here we show that in the coding regions of vertebrates both GC content and codon occurrences are strongly correlated with such "motif preferences" even though we quantify the latter using an index that is not affected by the base composition, codon usage, and protein-sequence encoding.

The gene arrangement, base composition, codon usage and tRNA structure of A. planci are similar to those of A. brevispinus.

The base composition, codon usage, and nucleotide substitution were analyzed with Mega 4.0 [ 68] and DAMBE 5.0.59 [ 69].

The mutation model used in the YN00 method accounts for the biases in base composition, codon usage, and transition/transversion rate.

Our results show that gene content, gene arrangement, base composition, codon usage, and mitochondrial transcription termination factor sequences are highly conserved in pentatomoid species, especially for species in the same family.

We present the first comparative analysis of eleven pentatomoid mitogenomes and our results show that gene content, gene arrangement, base composition, codon usage, RNA structure, and mitochondrial transcription termination factor sequences are highly conserved in pentatomoids, especially among closely-related species.

Nucleotide compositions, codon usage (excluding stop codons) and Relative Synonymous Codon Usage (RSCU) were calculated with MEGA 4.0 [ 47].

Base composition and codon usage were calculated using the DNA Stats and codon usage features available from the Sequence Manipulation Suite (http://www.bioinformatics.org/sms2/dna_stats.html).html

We confirmed that the phylogeny was not affected by base composition or codon usage bias; rhs from the same clade but different genomes had dissimilar base composition and codon usage scores, while rhs from different clades but the same genomes, for instance rhs from Yersinia spp., had similar codon usage scores (data not shown).

These charge-changing substitutions do not appear to be derived from differential neutral evolution of base composition or codon usage between Pgi-1 and Pgi-2 genes, as demonstrated by the fact that GC content and codon usage frequencies are not significantly different between Pgi-1 and Pgi-2 (GC content: P = 0.0782, Mann-Whitney U test, n = 12; rank order of codon usage: rs = 0.9509, n = 64).

Analysis of the A. dehalogenans strain 2CP-C genome for evidence of gene acquisitions via HGT was based upon base composition and codon usage patterns [95], [96].