Sentence examples for based upon sequence alignment from inspiring English sources
One noticeable feature regarding HupBMtb, based upon sequence alignment of HU orthologs from different bacteria, was the presence at its C-terminal end a highly basic extension (Supplementary Figure S1), designated as the C-terminal region (CTR), which prompted us to examine its role.
Based upon sequence alignments of Vig1 and Cig5, this family of enzymes was proposed to belong to the radical SAM superfamily, hence the alternative name RSAD2 or radical SAM containing domain 2, due to the presence of four conserved motifs commonly observed in other radical SAM enzymes.
However, even though this study incorporate the analysis of the rate and asymmetry in gene expression and polymorphisms, this study didn't improve the assessment of asymmetry in sequence evolution since the methodology used in this study is still based upon the sequence alignment.
A radial phylogenetic tree, created based upon multiple sequence alignment with hierarchical clustering (Corpet, 1988), showed that all the IpgB2-like A/E effectors indeed cluster with IpgB2 and are distant from IpgB1 and Map (Fig. 1B).
A phylogram based upon multiple sequence alignment with hierarchical clustering (Mackey et al., 2002) shows that EspT is divergent from the EspM/IpgB2 and does not cluster well with either IpgB1 or Map (Fig. 1C).
Based on sequence alignment, 48 orthologous lncRNAs were obtained.
MAF among the 17 varieties was ≥0.13 for all of the SNPs based upon the initial sequence alignment to the 14× assembly.
While applications of PrimerProspector to date have focused on SSU rRNA primer design, PrimerProspector can be used for any nucleic acid sequences and allows users to design de novo primers based upon arbitrary multiple sequence alignments.
The unclassified category (99, 7.5% of total) represented ESTs for which a protein identity could be assigned based upon an alignment with known sequences, but the metabolic function of that sequence remained unknown.
