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<h1>Z-DNA Tracker Help Page</h1>
<p>Welcome to the Z-DNA Tracker, a specialized tool designed for the analysis and identification of Z-DNA regions within nucleic acid sequences. This tool is based on the methodologies and algorithms developed in the <a href="https://github.com/abcsFrederick/non-B_gfa">non-B_gfa</a> project and the <a href="https://nonb-abcc.ncifcrf.gov/apps/nBMST/default/">nBMST application</a> hosted by the National Cancer Institute. Our Z-DNA Tracker provides a user-friendly interface to analyze sequences for potential Z-DNA forming regions, contributing valuable insights into the structural dynamics and biological functions of these unique DNA conformations.</p>
<h2>Getting Started</h2>
<ol>
<li><strong>Sequence Input</strong>: Begin by inputting your DNA sequences into the tool. You can input multiple sequences at once for batch analysis. Ensure that your sequences are in a compatible format (e.g., FASTA).</li>
<li><strong>Analysis Parameters</strong>: Set the parameters for your analysis. While default settings are provided, you may adjust these based on your specific research needs or the recommendations from the underlying algorithms.
<ul>
<li><strong>Minimum sequence size</strong>: minimal length of searched sequences (equal or bigger than 10)</li>
<li><strong>Threshold</strong>: this is the minimum score of searched Z-DNA score (equal or bigger than 0)</li>
</ul>
</li>
<li><strong>Submission</strong>: Once your sequences and parameters are set, submit them for analysis. The processing time will vary depending on the complexity and number of sequences.</li>
</ol>
<h2>Score Calculation</h2>
<p>The Z-DNA Tracker calculates scores based on the propensity of sequence regions to form Z-DNA. The scoring system is as follows:</p>
<li><strong>C/G and G/C pairs</strong>: These pairs are highly indicative of Z-DNA formation and are awarded <strong>25 points</strong> each.</li>
<li><strong>G/T, T/G, C/A, and A/C pairs</strong>: These pairs have a lower propensity for Z-DNA formation but are still significant, each receiving <strong>3 points</strong>.</li>
<li><strong>Other pairs</strong>: Any other base pairs are considered forbidden in the context of Z-DNA formation and are awarded <strong>0 points</strong>.</li>
<p>This scoring system is designed to highlight regions within the DNA sequence that have a higher likelihood of adopting the Z-DNA conformation, based on the specific base pairings and their known propensities for such structural formations.</p>
<h2>Understanding Your Results</h2>
<p>Upon completion of the analysis, the Z-DNA Tracker presents the results in an intuitive format, including:</p>
<li><strong>Heatmap</strong>: A visual representation showing the distribution and intensity of potential Z-DNA forming regions across your sequences.</li>
<li><strong>Analysis Settings</strong>:
</li>
<li><strong>Analysis Results</strong>:
<ul>
<li>Z-DNAs found</li>
<li>Frequency on 1000 bp</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 detailed list of results includes the following columns:</p>
<ul>
<li><strong>Position</strong>: The starting position of the Z-DNA region within the sequence.</li>
<li><strong>Length</strong>: The length of the Z-DNA region.</li>
<li><strong>Sequence</strong>: The actual nucleotide sequence of the Z-DNA region.</li>
<li><strong>Z-DNA GC Richness</strong>: The GC content within the Z-DNA region, indicative of its stability and propensity for Z-DNA formation.</li>
<li><strong>Z-DNA GT Richness</strong>: The GT content within the Z-DNA region, which can also influence Z-DNA formation.</li>
<li><strong>Z-DNA Score</strong>: The overall score calculated based on the specific base pairings and their propensities for Z-DNA formation.</li>
<li><strong>Z-DNA score/10bp</strong>: The overall score normalized to 10 bp length.</li>