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The graphic alignment tool for comparative sequence analysis (GATA) was used to align the sequences and visualize the results [ 88].
To check the homology at Scaffold level we used GATA, a graphic alignment tool for comparative sequence analysis [ 17].
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Cy3 (gProcessedSignal) and Cy5 (rProcessedSignal) values were used to calculate log ratios; these values were used for all graphic alignments.
In addition to tabulated alignments, graphic alignments were generated and grouped in three tiers: 1) viral gene annotation, 2) viral transcriptomes, and 3) viral proteomes (legends of Figure 1 and Figure 2).
A Bio::Graphics-driven alignment graph provides an overview of the queries, any hits and their respective scores.
Dynamic Time Warping (DTW) is an algorithm to align temporal sequences with possible local non-linear distortions, and has been widely applied to audio, video and graphics data alignments.
It is suggested that basic features like the
Alignment graphics were generated with UGENE (Okonechnikov et al. 2012).
Description#, graphic display# and alignments# were set at maximum values allowed.
The parameters comprised SNV coverage of >10, variant probability of 75%, and ploidy set at 1. SNVs were subsequently subjected to a final manual review of the alignment graphics versus the variant calls for the nine genomes.
In addition, visual inspection of the consistency of the assembled contigs is enabled by several graphic representations of the alignment against the reference genome, e.g., through dot plots.
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