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].
To identify the evolutionary pattern of the FABP2, this study compared the nucleotide composition, codon usage, and the protein structures of the homologous genes from 14 animal species.
Gene length, nucleotide composition, codon usage of the 13 PCGs, and RNA secondary structure were compared among the seven dipluran mt genomes.
We analyzed the nucleotide composition, codon usage and genomic rearrangement of these two mitochondrial genomes and compared them with mitochondrial genomes of other hemipteran species.
Nucleotide composition, codon usage, and sequence statistics were analyzed with MEGA4 and different programs implemented in the Sequence Manipulation Suite [ 45].
The mutation model used in the YN00 method accounts for the biases in base composition, codon usage, and transition/transversion rate.
Subsequent comparative and systematic analysis of the nucleotide composition, codon usage, DNA molecular evolution, protein structure and the potential mutation sites were performed to provide information for future functional study of this gene.
It is therefore crucial to verify the correct taxonomic assignment of each sequence, especially in multi-gene phylogenetic inference, using phylogenetic congruence, nucleotide composition, codon usage and, if necessary, additional wet experiments.
