Sentence examples for was aligned based on from inspiring English sources

A nucleotide alignment, which was used for the phylogenetic analysis, was aligned based on the deduced amino acid sequences using Clustal W. A general time reversible model with invariable sites and a gamma distribution for variable rate sites (GTR+I+G) was used.

This subset of sequences was aligned based on amino acid sequences and reverted back to nucleotide sequences.

The nucleotide sequence of the RDRP genes from sigma viruses and other rhabdoviruses was aligned based on the translated amino acid sequence using C lustalW.

For each gene of the selected data set, the nucleotide sequence was aligned based on the amino acid sequence using tranalign/EMBOSS package http://emboss.sourceforge.net/.net/

The region around the 3' end of the gene was aligned based on the position of the termination codons (UGA), and a sequence logo was created using WebLogo [ 107].

To calculate dN/dS ratios, nucleic acid sequence was aligned based on translated amino acids using MEGA4 http://www.megasoftware.net/[ 43], and ratios were calculated using the MEGA4 implemented Nei-Gojobori method with Jukes-Cantor correction.

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].