GC Skew and origin of replication-related plots for all Archaea genomes.

<p>We generated data and plots exhaustively for all Archaea complete genomes in the <a href="https://www.ncbi.nlm.nih.gov/datasets/genomes/?taxon=2157">NCBI dataset </a>in April 2022.</p> <p>Plots and data available:</p> <p><strong>SkewI and GC Skew:</strong></p> <ul> <li> <p>&nbsp;<strong>SkewI</strong>&nbsp;and&nbsp; <strong>GC content</strong> of every archaeon complete genome.</p> </li> <li> <p><strong>Cumulative GC Skew plot</strong> of every&nbsp;complete genome, with <strong>an estimation of the origin and termination</strong> point in the sequence, <strong>obtained by analyzing the plot</strong></p> </li> <li> <p>The same results are available sorted by taxonomy (Euryarchaeota, Crenarchaeota, Thaumarchaeota) and SkewI values.</p> </li> </ul> <p>&nbsp;</p> <p><strong>Dot Plots:</strong></p> <ul> <li> <p><strong>Dot plots</strong>&nbsp;comparing two by two each of the ten genomes having the highest SkewI value for any given taxonomy. An <strong>estimation of the origin of replication</strong> based on the cumulative GC Skew is represented.</p> </li> <li> <p>Dot plots comparing two by two a genome of <strong>high SkewI </strong>with a genome of <strong>low SkewI</strong>.</p> </li> </ul> <p>&nbsp;</p> <p><strong>Clinker</strong>:</p> <ul> <li> <p><strong>Comparison of genes around origin/terminus of replication within a taxonomy</strong>. Results obtained by running <strong>Clinker</strong>&nbsp;on a portion of 20 000 nucleotides before and after the origin/terminus of replication of all genomes belonging to the taxonomy.</p> </li> </ul> <p>&nbsp;</p> <p><strong>Violin plots</strong>:</p> <ul> <li> <p>Visual representation of the repartition of SkewI and GC Skew in different taxonomies of archaea and selected bacteria.</p> </li> <li> <p>Similar plots for <strong>TA skew</strong>,&nbsp;<strong>cumulative skew per codon position</strong> and&nbsp;<strong>cumulative skew for non-coding regions.</strong></p> </li> </ul> <p>&nbsp;</p> <p>Please refer to the readme file for further information about the results and references.</p>