Sentence examples for been aligned based on from inspiring English sources

Nucleotide divergences were calculated using the Kimura two-parameter method and the numbers of synonymous substitutions (dS) and nonsynonymous substitutions (dN) were calculated using the Nei and Gojobori (1986) [ 29] codon model for the nucleotide sequences that had been aligned based on amino acid position.

The codeml program of the PAML software package was used to detect positive selection in the CYP71C subfamily [ 39]. cDNA sequences were aligned based on protein alignment by using the RevTrans 1.4 server [ 40].

The DNA sequences were aligned based on the protein alignment.

Nucleotide sequences were aligned based on amino acid alignments using MUSCLE 3.6 [ 88].

The nucleotide sequences were aligned based on amino acid alignment using PRANK by applying the TranslatorX perl script [ 43].

The protein-coding DNA sequences were aligned based on their protein alignments at the web server http://www.bork.embl.de/pal2nal/[ 27].

Protein-coding DNA sequences (CDS) were aligned based on the protein alignments in the DAMBE with the default parameters, then converted the CDS alignments into PAML format for further analyses [ 67, 68].

The corresponding nucleotide sequences for these protein-coding genes were aligned based on indels inferred from the protein alignment; the web-based tool RevTrans [ 57], was used to place the indels in the nucleotide sequences.

Nucleotide sequences of selected subgroups of Rab proteins were aligned based on corresponding amino acid alignments.

All PCGs were aligned based on amino acid sequence alignments in MEGA version 4.0 [ 41].

Thereafter, the nucleotide sequences were aligned based on the protein sequence alignment profile using PAL2NAL [ 61].