Sentence examples for based on nucleotide alignments from inspiring English sources
We analyzed this subset of data based on nucleotide alignments of the KS region.
We contrasted our findings to the EnsEMBL compara database, which reports pairwise conserved synteny relations based on nucleotide alignments.
A maximum parsimony (MP) analysis based on nucleotide alignments (data not shown) grouped V. destructor (Parasitiformes) within the Acariformes, close to D. pteronyssinus.
Our approach to furthermore determine gene homology by calculating phylogenetic similarities based on nucleotide alignments (Additional Files 1 and 2) resulted in unrooted phylograms (Additional Files 3 and 4) of sparse information content due to low posterior probability values for C. vulgaris samples.
In order to compare the RNAcode predictions, which are based on nucleotide alignments, with the protein sequences from SwissProt and our peptide data, we blasted all peptide sequences (TBLASTN, E-value 10−3 and 98% identity) against the E. coli genome.
After Nucmer alignment, de novo assembled scaffolds of X. couchianus and X. hellerii were placed using a custom Perl script based on nucleotide alignment position of X. couchianus and X. hellerii scaffolds relative to the X. maculatus chromosomes.
Shown in Figure 5 is an unrooted phylogeny based on nucleotide sequence alignments (see Supplemental File S4 for the entire alignment and the model and parameters used for phylogenetic reconstruction).
Chiari et al. [ 13] used concatenation and MP-EST with multi-locus bootstrapping on two sets of gene trees - one based on amino acid (AA) and the other based on nucleotide (NT) alignments.
Ongoing genomic diversification of these begomoviral-satellite complexes was evident based on nucleotide sequence alignments, and analysis of single nucleotide polymorphisms, both factors that created new challenges for primer design.
Phylogenetic analysis based on nucleotide sequence alignment of the complete VP1 gene of 23 representative strains of HEV71 from southern Vietnam showed that they belonged to 3 subgenogroups, C1, C4, and to the previously undescribed subgenogroup C5.
Intron insertion-sites were determined manually, based on nucleotide and amino-acid alignments of cox 1 sequences.
