Sentence examples for alignment of virus from inspiring English sources

Evolutionary models selected with jModelTest were Tamura-Nei 93 + I + G (accounting for rate heterogeneity across sites via a Gamma distribution with a 0.327 alpha parameter and including 41% of invariant sites) for hosts (18S + ITS), and CpREV + G + F (using observed AA frequencies, and a 0.78 alpha parameter) for the alignment of virus protein sequences.

Broadening the outgroup to include GB virus A and GB virus C was not possible because the alignment of these viruses to HCV was poor.

We refer to the alignment of all viruses as the full alignment.

The ranks based on distances inferred from phylogenetic trees correlated with the rates based on Hamming distance (r = 0.93, p < 0.001 in the alignment of all viruses and r = 0.94, p < 0.001 in the HIV-1/SIVcpz alignment).

The vast sequence divergence among different virus groups has presented a great challenge to alignment-based analysis of virus phylogeny.

PCR was performed on the RNA with primers to amplify the entire HA and NA genes (designed based on alignment of several H1N1 viruses).

For the linear epitope recognized by AVFluIgG01, alignment of the H5N1 viruses HA1 used in MN assays revealed that GD/1/06 HA1 differed in 2 amino acids (S123P, D183N) from the wild-type AH/1/05 and/or other clade 2.3 H5N1 viruses, thereby providing important insight as to the location of the linear epitope.

To elucidate sequence information from 1 of the 13 isolates, we used a consensus-degenerate hybrid oligonucleotide primer algorithm to design degenerate PCR primers based on highly conserved amino acid sequences within multiple sequence alignments of all viruses in the subfamily Pneumovirinae (3 ).

The first data set comprises an alignment of 69 human influenza A/H3N2 virus haemagglutinin (HA) sequences (987 nt in length) isolated between 1981 and 1998.

A phylogenetic tree derived from the amino acid alignment of these sequences shows Kupe virus most closely related to DUGV (82.8% nt identity/95.9% aa identity), NSDV (74.9%/92.5%), CCHFV (71.9%/88.4%), and HAZV (71.7%/87.8%).

To amplify a 590-bp fragment of the G gene of RABV, the primer set Gp2L (5′-AGT AGGGGGG AAG AGA GCA TCC A-3′) and Gp2P (5′-GAG GAGGAAC AAC AAC TCC AT-3′), corresponding to nt 3957 4547 of the PV reference strain (accession no. M13215) of RABV was designed based on the alignment of sequences of different rabies virus isolates published in GenBank.