Sentence examples for alignment to represent from inspiring English sources
These studies use a multiple sequence alignment to represent the evolutionary history of a protein, gene, chromosome, or genome.
Filters for percent identity (6) and contig inclusion (7, also see Stage 1.1) are used to filter candidates based on the confidence with which Barnacle chose alignments to represent the genomic source(s) of the contig associated with the candidate, when creating the candidate in Stage 1.
So, class-5 alignments appear to represent suboptimal alignments with respect to the DIALIGN score.
We define this population by the preliminary alignment, taken to represent the phylogenetic diversity in Silene.
We repeated simulations with three different codon frequency spectra obtained for chicken turkey zebra finch orthologous alignments chosen to represent GC-poor, GC-average, and GC-rich genes.
Such results suggest the MC sequence region alignment to eIF4E represents a spurious PSI-BLAST hit between sequences displaying chance similarity.
The two S. bicolor alignments and two of the P. trichocarpa alignments were shorter than 80 bases and covered less than 12% of the contig, suggesting the alignments are unlikely to represent Populus or Sorghum but may be plant contamination of some kind.
Several studies showed that potential ncRNAs in genomic sequence have altered their primary sequence while maintaining their secondary structure and the sequence-based alignments are insufficient to represent the RNA structure across related species (Torarinsson et al., 2006, 2008).
Finally, we decide if the alignment is more likely to represent a protein-coding region or a non-coding region based on the log-likelihood ratio.
The algorithm for the alignment of two graphs and reconstruction of a new graph to represent this alignment is given in the Supplementary Material.
One of the most common ways to represent an alignment is using the familiar row and column matrix format of sequence alignments using the single letter abbreviations for residues (Fig. 1).
