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        <h1>CpX Islands Analysis Tool Help</h1>
    <p>This tool is a prototype implementation of an algorithm to find CpX islands within DNA sequences, where "X" can be any nucleotide (G, A, T, or C). The tool is based on <a href="https://www.pnas.org/doi/10.1073/pnas.052410099">Takai and Jones’ algorithm</a> and the prototype implementation, which can be found here: <a href="https://github.com/antroit47/cpg_islands">https://github.com/antroit47/cpg_islands</a></p>

    <h2>What are CpX Islands?</h2>
    <p>CpX islands are regions with a high frequency of CpX dinucleotides in genomic DNA, where "X" represents any nucleotide. These regions can be associated with gene promoters and are crucial in the regulation of gene expression.</p>

    <h2>How to Use the Tool</h2>
    <p>To analyze your DNA sequences for CpX islands, follow these steps:</p>
    <ol>
        <li>Adjust the analysis parameters as needed (see below for details).</li>
        <li>Select your DNA sequence(s) in the provided field.</li>
        <li>Review the output results displayed on the screen.</li>
    </ol>

    <h2>Input Parameters</h2>
    <p>The tool allows you to customize the analysis through various parameters:</p>
    <ul>
        <li><strong>Minimal Window Size:</strong> The smallest bp size of the window that can be considered an island (default 200).</li>
        <li><strong>Minimal CX Percentage:</strong> The minimum required nucleotide content of C and G (default 50%), where "X" is the nucleotide of interest (default 0.6).</li>
        <li><strong>Minimal Observed/Expected CpX:</strong> The minimum required value of observed to expected CpX dinucleotides, where "X" is the nucleotide of interest (default 0.6).</li>
        <li><strong>Minimal Island Merge Gap:</strong> The smallest bp gap between two islands which will cause them to merge into one (default 100).</li>
        <li><strong>First Nucleotide:</strong> The first nucleotide of the island (always "C").</li>
        <li><strong>Second Nucleotide:</strong> The second nucleotide of the island, which can be "G", "A", "T", or "C" (default "G").</li>
    </ul>

    <h2>Output Parameters</h2>
    <p>Upon completion of the analysis, the CpX islands tracker presents the results in an intuitive format, including:</p>
    <ul>
        <li><strong>Heatmap</strong>: The heatmap shows the amount of hits in precalculated segments.</li>
        <li><strong>Analysis Settings</strong></li>
        <li><strong>Analysis Results</strong>:
            <ul>
                <li>Islands found</li>
                <li>Frequency</li>
            </ul>
        </li>
        <li><strong>Export Options</strong>: Results can be exported in CSV and Bedgraph formats for further analysis or record-keeping.</li>
        <li><strong>Sequence Info</strong></li>
    </ul>
    <p>The output of the tool includes detailed information about the identified CpX islands:</p>
    <ul>
        <li><strong>Island Start and End Positions:</strong> The genomic coordinates of each identified CpX island.</li>
        <li><strong>Sequence</strong>: The actual nucleotide sequence of the CpX island.</li>
        <li><strong>CX Percentage:</strong> The percentage of selected base pair within the island.</li>
        <li><strong>Observed/Expected CpX Ratio:</strong> The ratio of observed to expected CpX dinucleotides in the island. Calculated as <math xmlns="http://www.w3.org/1998/Math/MathML">
  <mi>expCpg</mi>
  <mo>=</mo>
  <mfrac>
    <msup>
      <mrow>
        <mo>(</mo>
        <mfrac>
          <mi>C_Count + X_Count</mi>
          <mn>2</mn>
        </mfrac>
        <mo>)</mo>
      </mrow>
      <mn>2</mn>
    </msup>
    <mi>windowSize</mi>
  </mfrac>
  <mo>;</mo>
  </math>
  <math xmlns="http://www.w3.org/1998/Math/MathML">
  <mi>obsExp</mi>
  <mo>=</mo>
  <mfrac>
    <mi>CpX_Count</mi>
    <mi>expCpg</mi>
  </mfrac>
  <mo>;</mo>
</math>
</li>
        <li><strong>Island Length:</strong> The total base pair length of the CpX island.</li>
    </ul>
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