<p>The plot is from <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575466/pdf/cc-12-379.pdf">this publication, see page 2</a> the bottom of the plot with ACTG letters in different colours and sizes.</p>

<ol>
	<li>Could anyone clarify in layman&#39;s terms what it represents?</li>
	<li>More importantly, how do we plot it using R or any other tools?</li>
</ol>

<p>Here is the plot, if you can&#39;t access the paper:</p>

<p><img alt="" src="https://dl.dropboxusercontent.com/u/32553873/StackOverflow/Dennisplot.PNG" style="height:198px; width:390px" /></p>

<p>Found related post at SO: <a href="http://stackoverflow.com/questions/5438474/plotting-a-sequence-logo-using-ggplot2">Plotting a &ldquo;sequence logo&rdquo; using ggplot2?</a></p>

<p>That type of plot is called Sequence Logo. The X axis represent the nucleotide positions of a sequence, and the Y the entropy of each possible nucleotide. The size of each letter indicates how frequently it is found at that position: for example position 8 is almost always an A, while position 5 can be a T or C.</p>

<p>You can create sequence logos from a web interface using a popular application called <a href="http://weblogo.threeplusone.com/">WebLogo</a>, or using R packages such as <a href="http://bioconductor.org/packages/release/bioc/html/seqLogo.html">SequenceLogo</a>.</p>
