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<div class="container">
<h1>Z-DNA tracker help</h1>
<p>
This algorithm is a re-implementation of algorithm based on R-loop detection algorithm called
<a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">QmRLFS finder</a>. R-loop tracker is a toll for prediction of
R-loops in nucleic acids. The algorithms search for R-loop initiation zone based on presence of G-clusters and
R-loop elongation zone containing at least 40% of Guanine density. Our tool offers integration with Genome
browser, enhanced visualization and export formats, as well on-line sorting, and statistical characteristic.
Thanks to new java-based architecture can process whole chromosomes as well as complete genomes by batch analyses.
</p>
<h2 id="input">Input data</h2>
<hr />
<p>
Sequence can be imported as a text, fasta file or directly from NCBI database, for details please check help part
for <a href="/#/help/import">Import</a>. The choices are described in
<a href="/adoc/sequence.html">documentation</a>.<br /><br />
If you want to integrate your analysis with Genome browser, you need to provide information about the location of
the sequence in the genome. The name of the sequence has to have the following format:
<br /><br />
<code>
<Organism>_chr<number-of-chromosome>:<sequence-start>-<sequence-end>
</code>
<br /><br />
example of such name is as follows:<br /><br />
<code>
Human_chr8:128748315-128753680
</code>
<br /><br />
The organism's first letter must be capital (upper-case). This is ideal format, which will result in smooth import
into Genome browser.
</p>
<h2>Model selection</h2>
<hr />
<p>On the analysis page, you can select one of 2 models.</p>
<ul>
<li>
<b>RIZ 3G-cluster</b> RIZ (R-loop initiation zone) consists of <b>three</b> consecutive G-clusters which have at
least <b>3</b> Guanines in them.
</li>
<li>
<b>RIZ 4G-cluster</b>RIZ (R-loop initiation zone) consists of <b>two</b> consecutive G-clusters which have at
least <b>4</b> Guanines in them.
</li>
</ul>
<p>
Both of the models are described in <a href="https://pubmed.ncbi.nlm.nih.gov/25883153/">this article</a>.<br />
You can of course select both of the models at once.
</p>
<h2>Output formats</h2>
<hr />
<h3>Website</h3>
Website offers visualization of R-loop distribution in analyzed sequence. Each sequence is coloured: red is used for
Gs and blue for Cs. Brighter tone is used for longer Gs/Cs sequences. Results are shown as a table with following
sortable columns:
<ul>
<li><b>Position</b></li>
- start of the R-loop in given sequence
<li><b>Length</b></li>
- length of the R-loop
<li><b>Model</b></li>
- which model was used to detect the R-loop
<li><b>Strand</b></li>
- DNA strand (direction)
<li><b>RIZ</b></li>
- R-loop initiation zone sequence
<li><b>Linker length</b></li>
- length of a linker (0 if none is detected)
<li><b>REZ</b></li>
- R-loop elongation zone sequence. Altogether, RIZ+linker+REZ represents the whole R-loop
<li><b>RIZ Guanine richness</b></li>
- percentage of Guanine in RIZ area
<li><b>Rloop Guanine richness</b></li>
- percentage of Guanine in whole R-loop
<li><b>Number of 3G clusters</b></li>
<li><b>Number of 4G clusters</b></li>
<li><b>Number of 5G clusters and more</b></li>
</ul>
<h3 id="file-export">File export</h3>
All results can be exported into two possible file formats:
<ol>
<li>
<b>CSV</b> common file format with the following fields:
<ul>
<li>
position, length, RIZ, linker, REZ, model, strand (same as on website)
</li>
<li>
RIZGRICHNESS (percentage of Guanine nucleotides in RIZ sequence)
</li>
<li>
RLOOPGRICHNESS (percentage of Guanine nucleotides in whole R-loop)
</li>
<li>
G3 (count of 3G clusters in the sequence)
</li>
<li>
G4 (count of 4G clusters in the sequence)
</li>
<li>
GN (count of 5G and more clusters in the sequence)
</li>
</ul>
</li>
<li>
<b>bedGraph</b>
<br />
BedGraph is a special
<a href="https://genome.ucsc.edu/goldenPath/help/bedgraph.html">file format for Genome Browser integration</a>.
We have to improve our score rating for R-loops, which will result in better visualisation in Genome Browser.
<br />
In order to integrate your analysis into <a href="https://genome.ucsc.edu/">Genome Browser</a>, you have to
follow these steps:
<ol>
<li>
Navigate to the <a href="https://genome.ucsc.edu/cgi-bin/hgCustom">Custom tracks page</a> (Home -> My Data
-> Custom Tracks)
</li>
<li>Upload the bedGraph file downloaded from DNA analyser and hit the <code>Submit</code> button</li>
<li>
You should see the table with your track and now You can view it in Genome Browser (after hitting
<code>Go</code> button
</li>
<li>
The tracks will have green color shade according to their score and the track itself will be named
DNA-analyser
</li>
</ol>
</li>
</ol>
<h3>Example</h3>
The most basic example is to use the pre-imported sequence <code>Myc_chr8:128748315-128753680</code> available when
you are not logged in. You can find already imported sequences in the navigation by clicking on
<a href="/#/analyse/rloopr">Analyses -> R-loop tracker</a>. If you do not see the sequence, try logging out
beforehand. After this, just hit the green <b>Analyse</b> button, which starts the <em>RIZ 3G-cluster</em>
analysis for you.
<h4>Troubleshooting</h4>
If the track does not upload succesfully, try to follow the name specification described in
<a href="#input">Input section</a>.
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