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Expand Up @@ -29,75 +29,35 @@ <h2 class="project-tagline">A Software Framework for Database-Integrated Genome


<h3>
<a id="the-digs-tool" class="anchor" href="#the-digs-tool" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Explore uncharted genomic territory using BLAST and a relational database</strong>
<a id="the-digs-tool" class="anchor" href="#the-digs-tool" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Explore the dark genome using BLAST and a relational database</strong>
</h3>
<hr>



<p>
This website provides information about the <strong>DIGS tool</strong> - a software framework
for implementing <strong>database-integrated genome-screening (DIGS)</strong>.

</p>
<img src="./website/assets/images/logo_digs.png" align="right" alt="" width="340" />

<p>

<strong>Systematic, sequence similarity search-based genome screening</strong> is a powerful
approach for identifying and characterising genome features in silico.
</p>


<p>

<strong>DIGS</strong> is an approach for performing comparative genomic research <i>in silico</i>.
It entails using sequence similarity search tools
(e.g. <a target="_blank" href="http://blast.ncbi.nlm.nih.gov/Blast.cgi"><b>BLAST</b></a>)
to recover sets of related nucleotide sequences from molecular sequence databases,
then using a relational database (in combination with other analysis tools)
to further investigate these data.


</p>

<br>



<p><img src="./website/assets/images/digs-screenshot.png" alt="DIGS screenshot" /></p>


<blockquote>
<b>Database integrated genome screening</b>: the screenshot above shows
querying of a <b>DIGS project database</b> via the
<a target="_blank" href="https://www.sequelpro.com/"><strong>SequelPro</strong></a>
SQL client.
The screening database shown here contains the results of a broad screen
across mammalian species to identify rare 'endogenous lentivirus'
sequences, such as 'rabbit endogenous lentivirus K'
(<a target="_blank" href="https://doi.org/10.1073/pnas.0700471104">RELIK</a>).
The panel on the left shows the screening database tables, reflecting the
standard schema of a DIGS project database.
The uppermost panel contains a database query, written in
<a target="_blank" href="https://www.w3schools.com/sql/"><strong>structured query language (SQL)</strong></a>
- a standard language for storing, manipulating and retrieving data in databases.
The main panel shows the subset of the database entries returned by the query.
The SQL query shown here uses a
<a target="_blank" href="https://www.w3schools.com/sql/sql_where.asp"><b>'WHERE clause'</b></a>
to filter results.
</blockquote>

<strong>Database-integrated genome-screening (DIGS)</strong> is a form of systematic genome screening
in which a sequence similarity search-based screening pipeine is linked to a <strong>relational database management
system (RDBMS)</strong>. This provides a robust foundation for implementing large-scale, automated screens,
and allows screening output to be investigated via database-querying.
</p>

<h3>
<a id="author" class="anchor" href="#author" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Author</strong>
</h3>

<hr>
<p><a target="_blank" href="https://giffordlabcvr.github.io/virus-evolution/">Robert J. Gifford</a> (<a href="mailto:[email protected]">[email protected]</a>)</p>
<p>
This website provides information about the <strong>DIGS tool</strong> - a software framework
for implementing DIGS.
</p>

<h3>
<a id="license" class="anchor" href="#license" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>License</strong>
</h3>
<hr>

<p>
This project is licensed under the <a href="https://www.gnu.org/licenses/agpl-3.0.en.html">GNU Affero General Public License v. 3.0</a>.
</p>

<footer class="site-footer">
<span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/DIGS-tool">DIGS</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>
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