Sentence examples for using this alignment from inspiring English sources

Using this alignment as a template, nucleotide sequences were aligned with the GeneDoc program.

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).

A combined shape and feature overlap for the conformer pair using this alignment is then computed as following: (8).

3D models were calculated with the homology modeling software MODELLER [54] (version 9.5) using this alignment.

Bayesian analyses using this alignment produced a phylogeny with fairly high support for both the backbone nodes and the internal branches (Fig. 2).

A maximum likelihood (ML) phylogeny constructed using this alignment confirmed the relationship between the 54 UK sequences and South American isolates, disclosing a well-supported monophyletic group comprised exclusively of subtype C pol genes sampled in East Africa, Brazil and the UK (Figure S1, Figure S2).

Using this alignments, two sets of phylogenetic trees were constructed, neighbor-joining trees with bootstraps, and maximum likelihood trees, totaling 736 tree sets (Fig.  1a,b).

To retrieve even more distant UlaGL sequences, we first constructed a structure-based sequence alignment using the superimposed homologous structures identified with PDBeFold [ 30] (see below) and used this alignment, with 5 sequences and 232 aligned amino acid residues, as seed for the calculation with HMMER v. 3.0 (http://hmmer.org/) of a profile hidden Markov model (HMM) [ 33].

Due to large genetic divergence between FIV from different species, alignment for coding regions of FIV used the program REVTRANS ver 1.4 [ 29] which takes a multiple sequence file, translates that file into amino acid residues, aligns the amino acids, and uses this alignment as the scaffold for nucleotide alignment.

These 67 translationally competent sequences were aligned using RevTrans, which is a program that takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this alignment as a scaffold for constructing the alignment of the corresponding DNA sequences [ 87].

The 67 DNA sequences with a single open reading frame were aligned with the aid of RevTrans software [ 87], which is a program that takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this alignment as a scaffold for constructing the alignment of the corresponding DNA sequences.