Similarity scores were based on initial tRNA alignments undertaken in MacVector that were subsequently adjusted by eye according to secondary structure features (stems vs. loops).
Subsequent alignment was undertaken using MUSCLE v 3.8.31 (Edgar 2004) and MK tests for each alignment were conducted using the R package (R Core Team 2011) Popgenome (Pfeifer et al. 2014).
Thus, TASR does not re-identify the majority (>70%) of this subset of false-positive SNVs originally detected by Shah and colleague in NGS data, which highlights its utility as a tool to validate variants computationally, post sequence alignment, before undertaking orthogonal methods of variant verification such as resequencing.
This process of alignment should be undertaken as rapidly as possibly, and its outcome should be communicated to internal stakeholders and external partners.
After alignment, manual adjustments were undertaken to further curate the alignment file.
In an attempt to understand the evolutionary origins of AFPs, sequence alignment studies have been undertaken.
In-silico analysis was also undertaken using alignments of homologous regions of other related pox viruses (members of the subfamily Chordopoxvirinae, including vaccinia virus and contagious pustular dermatitis (Orf) virus) to ensure that the regions targeted by these different primers were likely to be specific.
Direct sequencing of the entire mtDNA genome was undertaken [ 18]; alignment and variant calling were performed using SeqScape software (v2.1.1, Applied Biosystems) comparing changes to the GenBank reference sequence for human mtDNA (accession number NC_012920.1).
A smaller number of searches of program and parameter values were undertaken for the alignment of trimmed ovine BESs against the equine genome assembly.
Alignments of genome sequences were undertaken using LAGAN [ 17] or Shuffle-LAGAN programs [ 28] implemented through mVISTA http://genome.lbl.gov/vista/mvista/submit.shtml.shtml
Secondly, searches for the site of phosphorylation were undertaken by constructing alignments of the 10 amino acid residues surrounding the conserved histidine from all predicted HKs in each replicon, and using the alignment to create a profile.
