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Figure 3 | Virology Journal

Figure 3

From: Bioinformatic analysis suggests that the Orbivirus VP6 cistron encodes an overlapping gene

Figure 3

MLOGD statistics for BTV, AHSV, PALV and PHSV/YUOV alignments. Output plots from MLOGD used in the 'Test Query CDS' mode, applied to the ORFX region in BTV, AHSV, PALV and PHSV/YUOV sequence alignments. See [16] for full details of the MLOGD software. The null model comprises the VP6 CDS and the query CDS is ORFX. In each plot, the top panel displays the raw log(LR) statistics at each alignment position. There is a separate track for each reference – non-reference sequence pair (labelled at the right, together with the pairwise divergences; albeit not legible for the BTV alignment since it contains so many – i.e. 48 – sequences). Stop codons (of which there are none except 3' terminal ones) in each of the VP6 and ORFX reading frames, and alignment gaps for each sequence, are marked on the appropriate tracks. The second panel displays the Σtree log(LR) statistic at each alignment position, where 'tree' represents a phylogenetic tree – see [16]. The third and fourth panels display sliding window means of the statistics in the first and second panels, respectively. The fifth panel shows the locations of the null and alternative model CDSs (i.e. VP6 and ORFX, respectively). The sixth panel shows the summed mean sequence divergence (base variations per alignment nt column) for the sequence pairs that contribute to the Σtree log(LR) statistic at each alignment position. This is a measure of the information available at each alignment position (e.g. partially gapped regions have lower summed mean sequence divergence). The predominantly positive values in the fourth panel indicate that ORFX is subject to functional constraints, at the amino acid level, over the majority of its length.

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