Files and plots in the Virus Database:

The columns of the table contain links to the following files:

1. name: Species name.
   
   
2. sequences: List of the strains used. First strain is taken as the reference sequence.
   
   
3. alignment: Sequence alignment.
   
   
4. pairs: List of sequence pairs tracing round the perimeter of one possible phylogenetic tree (details).
   
   
5. known CDSs: Positions of known CDSs.
   
   
6. six-frame (null model = non-coding): The MLOGD six-frame plots (40 codon window, 10 codon step size), taking the null model to be that the whole genome is non-coding. In general, the known CDSs should show up as regions of positive signal. In overlapping CDS regions (e.g. in Hepatitis B Virus) there can be some confusion in the signal, depending on the respective read-frames.
   
   
7. six-frame (null model = known CDSs): The MLOGD six-frame plots (40 codon window, 10 codon step size), taking the known CDSs as the null model. In these plots, the known CDSs won't necessarily have a positive signal since they have already been taken into account in the null model. Extended regions of positive signal may indicate potential new CDSs, especially where there is an absense of stop codons. Note that if there are overlapping CDSs in the list of known CDSs, then only the first CDS will be used in the null model within the region of overlap; the second CDS should then show up as a positive signal (e.g. for the first Hepatitis B Virus alignment, the P gene (487..3018) is in the null model, so has a low or negative signal in the six-frame plot, while the overlapping S gene (1028..2230) is not in the null model, so has a positive signal in the six-frame plot).
   
   
8. annotated CDSs (null model = non-coding): This contains links to plots and statistics for each annotated known CDS. For each CDS, the null model is that the whole genome is non-coding, while the alternate model is that the annotated CDS is coding. For each CDS, there are tables of the MLOGD and other statistics, plots of the MLOGD statistic summed over the sequences and at single-nucleotide resolution, and Monte Carlo simulation statistics and plots.
   
   
9. annotated CDSs (null model = other CDSs): This contains links to plots and statistics for each annotated known CDS. For each CDS, the null model is that the CDS is non-coding but all the other known CDSs are coding, while the alternate model is that all the known CDS are coding. (For genomes with a single CDS, this is the same as 'annotated CDSs (null model = non-coding)'.) For each CDS, there are tables of the MLOGD and other statistics, plots of the MLOGD statistic summed over the sequences and at single-nucleotide resolution, and Monte Carlo simulation statistics and plots.
   
   
10. all non-annotated ORFs: This contains links to tables of the MLOGD and other statistics, and plots of the MLOGD statistic summed over the sequences and at single-nucleotide resolution, for each non-annotated start-stop ORF >= 40 codons in the reference sequence. For each ORF, the null model is that only the known CDSs are coding, while the alternate model is that both the known CDSs and the query ORF are coding.