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We performed an alignment compared with Arabidopsis thaliana (Supplementary Figure 1).
By comparing these two rich evolutionary models, PhyloCSF can observe many additional informative features of a given alignment compared with the d N / d S test.
This suggests that the collagen fibers in the adventitia of these mice exhibited increased thickness, density and alignment compared with their sham-treated counterparts.
The current study by Won and colleagues concluded that patients undergoing revision ACL surgery have a greater incidence of significant varus alignment compared with patients undergoing primary ACL reconstruction.
From these BLAST hits, only those were further analyzed that were starting from the first position of the query protein and were having at least one premature stop codon inside the alignment compared with the parent protein.
Incomplete alignments reflect the reduced sensitivity of pairwise alignment compared with the HMM based methods used to annotate the Pfam domains in RPD2, and the fact that in the diverse set of homologous RPD2 domains, half of the detectable homologs share <33% sequence identity.
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The evolution of local misorientations and microband structures were quantified by high-resolution electron backscatter diffraction in a field emission gun scanning electron microscope and their alignments compared with the traces of active slip planes and macroscopic shear stress planes.
Analysis of trees constructed from the RepA, RepB, RepC, TrbE, TrbK, TraI, TraR, TraM, TraG, and TraA protein alignments compared with the MAFFT alignments of each protein was accomplished by using the likelihood scores.
A number of studies have shown that the maximum likelihood approach can avoid systematic errors and makes more efficient use of information in the protein alignments compared with the counting approach [ 10].
Furthermore, it offers a sensitive version of the x-drop algorithm for seed-extension, which results in highly accurate alignments compared with the BLAST gold standard and our competitors.
"It would not be hard to compute an accurate time history of the tidal levels during those months to see just how anomalous were those few hours of critical alignment compared [with] a normal set of tides," Vidale told Life's Little Mysteries.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com