Sentence examples for basis of codon alignments from inspiring English sources
Then, sample I clusters were analyzed on the basis of codon alignments and sample II on that of protein alignments.
We estimated ω values by means of the codeml program in the PAML v4.4 package (Yang 1997) on the basis of multiple alignments of orthologous codon sequences and a tree topology.
Multiple sequence alignments of the deduced amino acids were used to generate codon alignments of the sequenced transcripts as described previously [ 4].
Then, multiple codon alignments of genes corresponding to protein sequence alignments were obtained using PAL2NAL [ 32].
Codon alignments of nucleotide sequences (Additional File 13) for three groups were constructed from the PAL2NAL server [ 83] based corresponding protein sequence alignments.
We created the nucleotide sequence alignments on the basis of amino acid alignments and calculated the nucleotide replacements in the form of 4 × 4 NRM, individually for three codon positions for three different groups of orthologs under study.
On the basis of each alignment, we partitioned substitutions by codon position and eliminated all non-LTR sequences with nonrandom distributions of substitutions across codon positions (χ test; P < 0.05).
Multiple NarJ subfamily member sequence alignments and their corresponding nucleotide codon alignments were used to identify regions of residue conservation.
Analysis of the synonymous/non synonymous substitution rates required construction of pairwise, codon aligned, sequence alignments.
Multiple sequence alignments were constructed on the basis of the pairwise alignments, those homologous sequences without miRNA features were excluded.
