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3 results for “GC Skew”
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> <strong>SkewI</strong> and <strong>GC content</strong> of every archaeon complete genome.</p> </li> <li> <p><strong>Cumulative GC Skew plot</strong> of every 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> </p> <p><strong>Dot Plots:</strong></p> <ul> <li> <p><strong>Dot plots</strong> 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> </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> 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> </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>, <strong>cumulative skew per codon position</strong> and <strong>cumulative skew for non-coding regions.</strong></p> </li> </ul> <p> </p> <p>Please refer to the readme file for further information about the results and references.</p>
SkewDB: A comprehensive database of GC and 10 other skews for over 28,000 chromosomes and plasmids
<p>GC skew denotes the relative excess of G nucleotides over C nucleotides on the leading versus the lagging replication strand of eubacteria. While the effect is small, typically around 2.5%, it is robust and pervasive. GC skew and the analogous TA skew are a localized deviation from Chargaff's second parity rule, which states that G and C, and T and A occur with (mostly) equal frequency even within a strand.</p> <p>Most bacteria also show the analogous TA skew. Different phyla show different kinds of skew and differing relations between TA and GC skew.<br> This article introduces an open access database (https://skewdb.org) of GC and 10 other skews for over 28,000 chromosomes and plasmids. Further details like codon bias, strand bias, strand lengths and taxonomic data are also included.</p> <p>The SkewDB database can be used to generate or verify hypotheses. Since the origins of both the second parity rule, as well as GC skew itself, are not yet satisfactorily explained, such a database may enhance our understanding of microbial DNA.</p>
SkewDB: A comprehensive database of GC and 10 other skews for over 28,000 chromosomes and plasmids
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