Sentence examples for using this alignment we from inspiring English sources

Using this alignment, we scored the 34 missense substitutions with Align-GVGD [ 43- 45] and SIFT [ 41, 42] (Supplementary Table S1 in Additional file 1).

Using this alignment, we divided the Geobacter CheRs into three groups.

Using this alignment, we can estimate the frequency, f pi, of each nucleotide i in each position of aligned sequences, p, which is the element of the PFM.

Using this alignment, we constructed a tree using maximum likelihood methodology (Guindon et al. 2010) and used the program Dendroscope (Huson, Richter et al. 2007) to present a phylogram.

Using this alignment, we examined the DDE/D signature in the A. castellanii sequences and found that the residues are located within conserved "DET," "DNA," and "PIE" motifs, indicative of Tc1/ mariner transposases [ 36, 44, 45] (Fig.  3a; Additional file 6: Figure S6).

We used this alignment to identify amino acid substitutions that correlated with mineralocorticoid sensitivity across GRs.

We used this alignment to make a HMM profile using the HMMER 3.0 utility hmmbuild [ 21, 22] which provides a model of homology for the cydX locus.

We use this alignment to make functional predictions, which turn out to be consistent with published gene expression data, as well as gene position and molecular weight.

Also notice that there may be nodes in q or d that are not aligned to any node by ϕ i. Phase II: if all the nodes of q are aligned at the end of Phase I, we simply use this alignment to compute LB i (q, d).

To create a maximum likelihood phylogenetic tree of the roo/ rooA elements from this alignment, we used PhyML_aLRT[ 27], a version of PhyML[ 28] that incorporates an approximate likelihood ratio test to estimate the statistical support of the tree topology.

Using these alignments, we obtained twelve features for each nsSNV.