Sentence examples for see alignment from inspiring English sources
The normal samples within E-MTAB-513 & GSE52194 have been downloaded as raw sequence data (.fastq files) and processed using STAR aligner [ 22] and htseq-count [ 23] (see alignment and gene expression quantification section).
Type I and II NLPs were aligned using ClustalW [ 44] with default parameters and gapopen = 0 (see alignment results in [ 45] and [ 46]).
However we cannot rule out that point mutations alone produced these changes (see alignment Figure 5c).
The final alignment of 11,615 characters was finished by manual adjustment (see Alignment S1).
<img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0005708.e003.PNG" class= inline-graphic"/> where ζ is the alignment score (see "Alignment" subsection below).
Instead, it shares high sequence similarity with proteins of Aeromonas salmonicida (53% amino-acid identity, Table 1) and various Bacillus species (including B. thuringiensis, B. cereus, and B. weihenstephanensis, 42 49% identity, see alignment in Supplementary Figure S1A).
The 109 genes in Table S1 display statistically supported incongruence with the organismal phylogeny on both SH and AU tests (see alignments in File S1).
Unfortunately, a closer scrutiny of the Phrap-generated assembly (e.g., the dot plots of the contigs' alignment) reveals that Phrap's apparent superiority is without much substance – Phrap's weaknesses, as evidenced by its mis-assemblies within long contigs (see alignments in Document S1), are not captured by the N50-like performance parameters.
Most variability is found within the N-terminal regions (also see alignments in the Additional file 2).
Most variability is found at the N-terminal region and most conservation is within the predicted transmembrane 3 (also see alignments in Additional file 2).
Most variability is found at the N-terminal region and within the proposed third intracellular domain, which carried length polymorphisms (also see alignments in Additional file 2).
