Sentence examples for use this alignment from inspiring English sources

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).

It was necessary to align many previously known fungal orthologs of Nbs1 and then use this alignment to analyze the C. cinereus genome.

Our approach was to first calculate a structure-based sequence alignment subset of the TFP structures in the receptor-like cluster, and then use this alignment to direct the alignment of a much larger representative set of TFP domain amino acid sequences (i.e. lacking 3D structures).

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.

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].

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

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.

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).

To identify C. cinereus nbs1, we searched by tBLASTn with several fungal orthologs and then aligned 25 fungal orthologs of Nbs1 and used this alignment to further search the C. cinereus genome by PSI-BLAST.