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The patterns of conservation in the TD using Consurf (Ashkenazy et al., 2010) analysis suggested that the highly conserved residues (score 9) tend to be clustered in two specific regions of the usher.
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The most highly conserved 25% of residues scored between −1.026 and −0.906, whereas the most poorly conserved 25% of residues scored between 0.589 and 2.811 (Fig. S2).
The TM-PRED program (http://www.ch.embnet.org/cgi-bin/TMPRED from parser; TM helix length between 17 and 33 residues; scores, >1,000) predicted that VtrA and VtrB would contain one TM region (VtrA, amino acids 134 153 and VtrB, amino acids 157 182), indicating that VtrA and VtrB are transmembrane transcriptional activators.
In Section 3.3, we present evidence that residues scored highest by the RF importance score may be less predictive than literature-derived feature sets.
In the CWM residues, scores for other species are mixed together (not separated), however, for tomato, which is characterized by one of the biggest values of pectin content in the CDTA supernatant, all scores lie on the positive side of PC2 axis.
Our proposed algorithm yields triclusters that have a mean-squared residue score below a threshold δ.
They are then sorted according to their mean squared residue score relative to the bicluster classifier.
Cheng and Church tried to identify submatrices of low mean residue score which indicates uniform fluctuation in expression profiles.
A sub-matrix with a mean squared residue score below a chosen threshold is termed a δ-bicluster.
Cheng and Church [ 6] define a bicluster as a submatrix having a low mean squared residue score.
Now extending this idea, here we present a novel definition of Mean Squared Residue score for 3D microarray gene expression datasets.
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