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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">

<head>
<title>RepeatExplorer server</title>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" href="style/base.css" type="text/css" />
<style type="text/css">
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padding: 5px;
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</style>
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<body lang="en-US" dir="ltr">
<img src="images/umbr_programs_icons/RE_header.png"
alt="Welcome to RepeatExplorer"
width="700px"/>

<!--<p style="color:red;font-size:160%;"><b>RepeatExplorer2 and TAREAN tools are currently being reinstalled are not available. We are sorry for any inconvenience caused.</b>
</p>-->
<p>Developed and maintained by the <a href="http://w3lamc.umbr.cas.cz/lamc/" target="_blank">Laboratory
of Molecular Cytogenetics</a>, Institute of Plant Molecular Biology,
Biology Centre CAS, Ceske Budejovice, Czech Republic</p>
<p>This RepeatExplorer Galaxy portal is a part of services provided
by <a href="https://www.elixir-czech.cz/" target="_blank">ELIXIR </a>
(European research infrastructure for biological information). Please
acknowledge this fact in your publications by adding a statement:
“<strong><i><span style="font-weight: normal">Computational
resources for RepeatExplorer analysis were provided by the ELIXIR-CZ
project (LM2023055), part of the international ELIXIR
infrastructure.</span></i></strong>”
</p>

<div class="frame">
<a href="http://www.elixir-czech.cz" target="_blank">
<span class="helper"></span>
<img align="middle" src="images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png" alt="ELIXIR"/>
</a>
</div>




<!-- <p>If <b>issue to open tools/history</b> (e.g. <i>[history_id=None] Failed to retrieve history..</i>) then please try to clean your browser cache and delete cookies or try to open new browser window in anonymous mode.
</p> -->
<hr/>


<h2 class="western">Resources</h2>
<ul>

<li>
<p style="margin-bottom: 0in"><a href="https://rdcu.be/b80Gr" target="_blank">Step by step protocols</a>
</p>

</li>

<li>
<p style="margin-bottom: 0in"><a href="http://repeatexplorer.org/" target="_blank">Documentation
and training information</a>
</p>

</li>
<li>

<p style="margin-bottom: 0in"><a href="http://repeatexplorer.org/?page_id=179" target="_blank">The
impact of genome coverage and sequence read sampling on
reproducibility of repeat identification</a></p>
</li>
<li>
<p style="margin-bottom: 0in">Official <a href="https://galaxyproject.org/" target="_blank">Galaxy
Project</a> website with information how to use the Galaxy platform
</p>
</li>
<li>
<p>For command line version of the RepeatExplorer tools, see
the source <a href="https://bitbucket.org/petrnovak/repex_tarean/" target="_blank">code
repository</a>
</p>
</li>
</ul>

<a href="https://twitter.com/RepeatExplorer?ref_src=twsrc%5Etfw" class="twitter-follow-button" data-show-count="false" data-size="small">Follow @RepeatExplorer</a>
<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<hr/>

<h2 class="western"><a href="news.html">Updates</a></h2>
<table cellpadding="5" cellspacing="5">
<tr>
<th class="date" style="border: none; padding: 0in"></th>
<th class="subject" style="border: none; padding: 0in"></th>
</tr>
<tr>
<td style="border: none; padding: 0in">
<p>Oct 23, 2020</p>
</td>
<td style="border: none; padding: 0in">
<h4 class="western">Step by step protocols were published in
<a href="https://rdcu.be/b80Gr" target="_blank">Nature Protocols</a></h4>
</td>
</tr>
<tr>
<td style="border: none; padding: 0in">
<p>Jan 13, 2020</p>
</td>
<td style="border: none; padding: 0in">
<h4 class="western">Galaxy server was updated to version 19.09</h4>
</td>
</tr>
<tr>
<td style="border: none; padding: 0in">
<p>Jan 13, 2020</p>
</td>
<td style="border: none; padding: 0in">
<h4 class="western">RepeatExplorer2 and TAREAN tools were updated
to version 2.3.7</h4>
<p>See changelog for detailed description of included changes.
Previous versions can be found in <i>Obsolete tools</i> section
</p>
</td>
</tr>
<tr>
<td style="border: none; padding: 0in">
<p>Jan 8, 2020</p>
</td>
<td style="border: none; padding: 0in">
<h4 class="western">RepeatExplorer tools are now available in
Galaxy toolshed</h4>
<p>Packages repeatexplorer2, dante and re_utils can be installed
from Galaxy toolshed to custom Galaxy instance if you prefer
analysis using RepeatExplorer on on your server.</p>
</td>
</tr>
<tr>
<td style="border: none; padding: 0in">
<p>Nov 10, 2019</p>
</td>
<td style="border: none; padding: 0in">
<h4 class="western">Data quota increased to 200G</h4>
<p>Data quota for registered users was increased from 50G to 200G
to enable easier analysis of larger datasets</p>
</td>
</tr>
</table>
<h3 class="western">Changelog
</h3>
<p style="margin-bottom: 0in">Information about changes in
RepeatExplorer programs can be found in its repository <a href="https://bitbucket.org/petrnovak/repex_tarean/src/devel/CHANGELOG.md" target="_blank">changelog.</a>
</p>
<hr/>

<h2 class="western">Contact information</h2>
<p style="margin-bottom: 0in">If you need a help or you want to
report a problem, please contact <a href="mailto:[email protected]">server
administrator</a>.
</p>
<hr/>

<h2 class="western">How to Cite</h2>
<p>Novak, P., Neumann, P., Macas, J. (2020) &#8211; <a href="https://rdcu.be/b80Gr" target="_blank">Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2</a>. <em>Nature Protocols </em><strong>15</strong>:3745–3776.</p>
<p>Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013)
- <a href="http://bioinformatics.oxfordjournals.org/content/29/6/792" target="_blank">RepeatExplorer:
a Galaxy-based web server for genome-wide characterization of
eukaryotic repetitive elements from next generation sequence reads.</a>
<i>Bioinformatics</i> <b>29</b>:792-793.
</p>
<p><i>Classification of repetitive elements using REXdb:</i></p>
<p>Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) –
<a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0144-1" target="_blank">Systematic
survey of plant LTR-retrotransposons elucidates phylogenetic
relationships of their polyprotein domains and provides a reference
for element classification</a>. <em>Mobile DNA</em> <b>10</b>:1.</p>
<p><i>The principle of repeat identification implemented in the
RepeatExplorer:</i>
</p>
<p>Novak, P., Neumann, P., Macas, J. (2010) - <a href="http://www.biomedcentral.com/1471-2105/11/378" target="_blank">Graph-based
clustering and characterization of repetitive sequences in
next-generation sequencing data.</a> <i>BMC Bioinformatics</i>
<b>11</b>:378.
</p>
<p><i>Using TAREAN for satellite repeat detection and
characterization:</i>
</p>
<p>Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann,
P., Macas, J. (2017) - <a href="https://doi.org/10.1093/nar/gkx257" target="_blank">TAREAN:
a computational tool for identification and characterization of
satellite DNA from unassembled short reads.</a> <i>Nucleic Acid
Research </i><b>45</b>:e111
</p>
<hr/>

<div class="frame">
<a href="http://www.elixir-czech.cz" target="_blank">
<span class="helper"></span>
<img align="middle" src="images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png" alt="ELIXIR"/>
</a>
</div>



<hr/>

<h2 class="western">Terms of Use
</h2>
<p>RepeatExplorer is provided as free, public, Internet accessible
service, in the hope that it will be useful, but WITHOUT ANY
WARRANTY. Data transfer are encrypted, but data storage are not. If
there are restrictions on the way your research data can be stored
and used, please consult your local institutional review board or the
project PI before uploading it to this Galaxy server. If you have
protected data, large data storage requirements, or short deadlines
you are encouraged to setup your own local Galaxy instance with
RepeatExplorer Alternatively, you can install only RepeatExplorer and
use its <em>command line version</em>. If you need help with
RepeatExplorer or you want to report a problem, please contact <a href="mailto:[email protected]">server
administrator</a>
</p>
<p><br/>
<br/>

</p>
</body>
</html>
</style>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<p><link rel="stylesheet" href="style/base.css" type="text/css" /></p>
<p><img src="images/umbr_programs_icons/RE_header.png"
alt="Welcome to RepeatExplorer"
width="700px"/></p>
<p>Developed and maintained by the <a href="http://w3lamc.umbr.cas.cz/lamc/">Laboratory of Molecular Cytogenetics</a>, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic</p>
<p>This RepeatExplorer Galaxy portal is a part of services provided by <a href="https://www.elixir-czech.cz/">ELIXIR</a> (European Research Infrastructure for Biological Information). Please acknowledge this fact in your publications by adding a statement: <em>“Computational resources for RepeatExplorer analysis were provided by the ELIXIR-CZ project (LM2023055), part of the international ELIXIR infrastructure.”</em></p>
<div class="frame">
<p><a href="http://www.elixir-czech.cz" target="_blank"> <span class="helper"></span> <img align="middle" src="images/umbr_programs_icons/ELIXIR_CZECHREPUBLIC_white_background_small.png" alt="ELIXIR"/> </a></p>
</div>
<hr />
<h2 id="contact-information">Contact information</h2>
<p>If you need help, need to increase a data quota, or want to report a problem, please contact <a href="mailto:[email protected]">server administrator</a>. If you encounter an error while running a tool, please report a bug using the bug icon in the dataset history.</p>
<hr />
<h2 id="resources">Resources</h2>
<ul>
<li><a href="https://rdcu.be/b80Gr">Step-by-step protocols</a> include four protocols on how to use main RepeatExplorer tools</li>
<li><a href="https://www.youtube.com/@repeatexplorer4803/videos">RepeatExplorer channel on YouTube</a></li>
<li><a href="http://repeatexplorer.org/">Documentation and training information</a></li>
<li><a href="http://repeatexplorer.org/?page_id=179">The impact of genome coverage and sequence read sampling on reproducibility of repeat identification</a></li>
<li>Official <a href="https://galaxyproject.org/">Galaxy Project</a> website with information on how to use the Galaxy platform</li>
<li>For the command line version of the RepeatExplorer tools, see the source <a href="https://github.com/kavonrtep/repex_tarean">code repository</a></li>
</ul>
<a href="https://twitter.com/RepeatExplorer?ref_src=twsrc%5Etfw" class="twitter-follow-button" data-show-count="false" data-size="small">Follow <span class="citation" data-cites="RepeatExplorer">@RepeatExplorer</span></a>
<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<hr />
<h2 id="common-use-cases-of-repeatexplorer-server">Common Use Cases of RepeatExplorer Server</h2>
<p>The RepeatExplorer server provides a suite of tools designed for the comprehensive analysis of repetitive DNA sequences in genomic data. Here are the most common use cases for utilizing these tools:</p>
<ul>
<li><p><strong>Annotation of repeats directly from low coverage sequencing</strong>: It can be accomplished using the RepeatExplorer2 tool. This approach is ideal for initial exploration and annotation of repetitive sequences using low coverage data (refer to protocol 1 in the step-by-step protocols above).</p></li>
<li><p><strong>Comparative analysis of repeats in multiple species from low coverage sequencing reads</strong>: Use protocol 2 for analyzing repetitive DNA across different species.</p></li>
<li><p><strong>Tandem repeat annotation from low coverage sequencing</strong>: If your focus is primarily on tandem repeats, use the Tandem Repeat Analyzer tool (TAREAN). See protocol 3 in the step-by-step protocols for details.</p></li>
<li><p><strong>Chip-Seq experiments</strong>: The ChIP-seq Mapper tool identifies centromeric repeats from CENH3 ChIP-seq data without the need for a complete genome assembly, leveraging assembled contigs from repeat clusters as a reference for mapping reads and highlighting significantly enriched repeats (refer to protocol 4).</p></li>
<li><p><strong>Annotation of full-Length LTR-retrotransposons in genome assemblies</strong>: For detailed annotation of LTR-retrotransposons within assembled genomes, use the DANTE + DANTE_LTR tools. (see <a href="https://github.com/kavonrtep/dante_ltr">https://github.com/kavonrtep/dante_ltr</a> for details)</p></li>
<li><p><strong>Annotation of tandem repeats in genome assemblies</strong>: The TideCluster tools are designed for the annotation and analysis of tandem repeats within genome assemblies (see <a href="https://github.com/kavonrtep/TideCluster">https://github.com/kavonrtep/TideCluster</a> for more information).</p></li>
</ul>
<hr>
<h2 id="how-to-cite">How to Cite</h2>
<p>Novak, P., Neumann, P., Macas, J. (2020) – <a href="https://rdcu.be/b80Gr">Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2</a>. <em>Nature Protocols</em> <strong>15</strong>:3745–3776.</p>
<p>Novak, P., Neumann, P., Pech, J., Steinhaisl, J., Macas, J. (2013) - <a href="http://bioinformatics.oxfordjournals.org/content/29/6/792">RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next-generation sequence reads</a>. <em>Bioinformatics</em> <strong>29</strong>:792-793.</p>
<p><em>Classification of repetitive elements using REXdb:</em></p>
<p>Neumann, P., Novak, P., Hostakova, N., Macas, J. (2019) – <a href="https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-018-0144-1">Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification</a>. <em>Mobile DNA</em> <strong>10</strong>:1.</p>
<p><em>The principle of repeat identification implemented in the RepeatExplorer:</em></p>
<p>Novak, P., Neumann, P., Macas, J. (2010) - <a href="http://www.biomedcentral.com/1471-2105/11/378">Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data</a>. <em>BMC Bioinformatics</em> <strong>11</strong>:378.</p>
<p><em>Using TAREAN for satellite repeat detection and characterization:</em></p>
<p>Novak, P., Robledillo, L.A.,Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) - <a href="https://doi.org/10.1093/nar/gkx257">TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads</a>. <em>Nucleic Acid Research</em> <strong>45</strong>:e111</p>
<hr>
<h2 id="terms-of-use">Terms of Use</h2>
<p>RepeatExplorer is provided as free, public, Internet accessible service, in the hope that it will be useful, but WITHOUT ANY WARRANTY. Data transfer are encrypted, but data storage is not. If there are restrictions on the way your research data can be stored and used, please consult your local institutional review board or the project PI before uploading it to this Galaxy server. If you have protected data, large data storage requirements, or short deadlines you are encouraged to set up your own local Galaxy instance with RepeatExplorer Alternatively, you can install only RepeatExplorer and use its <em>command line version</em>. If you need help with RepeatExplorer or you want to report a problem, please contact <a href="mailto:[email protected]">server administrator</a>.</p>
<hr>

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