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2 changes: 1 addition & 1 deletion index.html
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<p>

<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
in which a sequence similarity search-based screening pipeline 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.
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153 changes: 0 additions & 153 deletions website/user-guide/explore.html
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</p>




<br>
<h3>
<a id="Publications" class="anchor" href="#Publications" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Publications Utilising DIGS</strong>
</h3>
<hr>

<p>


Campbell M, Loncar S, Gifford RJ, Kotin R, and RJ Gifford
<b>(2022)</b>
<br>
Comparative analysis reveals the long-term co-evolutionary history of parvoviruses and vertebrates.
<br>
<i>Plos Biology</i>
<a href="https://doi.org/10.1371/journal.pbio.3001867" target="_blank">[view]</a>
<br>
<br>


Bamford CGG, de Souza WM, Parry R and RJ Gifford
<b>(2022)</b>
<br>
Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of the <i>Flaviviridae</i>.
<br>
<i>Virus Evolution</i>
<a href="https://doi.org/10.1093/ve/veac085" target="_blank">[view]</a>
<br>
<br>

Wickenhagen A, Sugrue E, Lytras S, Kuchi S, Noerenberg M, Turnbull ML, Loney C, Herder V, Allan J, Jarmson I, Cameron-Ruiz N, Varjak M, Pinto RM, Lee JY, Iselin L, Palmalux N, Stewart DG, Swingler S, Greenwood EJD, Crozier TWM, Gu Q, Davies EL, Clohisey S, Wang B, Trindade Maranhão Costa F, Freire Santana M, de Lima Ferreira LC, Murphy L, Fawkes A, Meynert A, Grimes G, Da Silva Filho JL, Marti M, Hughes J, Stanton RJ, Wang ECY, Ho A, Davis I, Jarrett RF, Castello A, Robertson DL, Semple MG, Openshaw PJM, Palmarini M, Lehner PJ, Baillie JK, Rihn SJ, and SJ Wilson
<b>(2021)</b>
<br>
A prenylated dsRNA sensor protects against severe COVID-19.
<br>
<i>Science</i>
<a href="http://dx.doi.org/10.1126/science.abj3624" target="_blank">[view]</a>
<br>
<br>

Lytras S, Arriagada G, and RJ Gifford
<b>(2021)</b>
<br>
Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes.
<br>
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/advance-article/doi/10.1093/ve/veab012/6157734" target="_blank">[view]</a>
<br>
<br>

Hildebrandt E, Penzes J, Gifford RJ, Agbandje-Mckenna M, and R Kotin
<b>(2020)</b>
<br>
Evolution of dependoparvoviruses across geological timescales – implications for design of AAV-based gene therapy vectors.
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/article/doi/10.1093/ve/veaa043/5842153">[view]</a>
<br>
<br>

Pénzes JJ, de Souza WM, Agbandje-Mckenna M, and RJ Gifford
<b>(2019)</b>
<br>
An ancient lineage of highly divergent parvoviruses infects both vertebrate and invertebrate hosts.
<br>
<i>Viruses</i>
<a href="https://www.mdpi.com/1999-4915/11/6/525" target="_blank">[view]</a>
<br>
<br>

Ito J, Gifford RJ, and Kei Sato
<b>(2019)</b>
<br>
Retroviruses drive the rapid evolution of mammalian APOBEC3 genes.
<br>
<i>PNAS</i>
<a href="https://www.pnas.org/content/early/2019/12/11/1914183116" target="_blank">[view]</a>
<br>
<br>

Shaw AE, Hughes J, Gu Q, Behdenna A, Singer J, Dennis T, Orton RJ, Varela M, Gifford RJ, Wilson SJ and M Palmarini
<b>(2017)</b>
<br>
Fundamental properties of the mammalian innate immune system revealed by multi-species comparison of type I interferon responses.
<br>
<i>Plos Biology</i>
<a href="http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.2004086" target="_blank">[view]</a>
<br>
<br>

Hron T, Elleder D, and RJ Gifford
<b>(2019)</b>
<br>
Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species.
<br>
<i>Retrovirology</i>
<a href="https://retrovirology.biomedcentral.com/articles/10.1186/s12977-019-0495-9" target="_blank">[view]</a>
<br>
<br>

Pénzes JJ, Marsile-Medun S, Agbandje-McKenna M, and RJ Gifford
<b>(2018)</b>
<br>
Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses.
<br>
<i>Virus Evolution</i>
<a href="https://academic.oup.com/ve/article/4/2/vey026/5179240" target="_blank">[view]</a>
<br>
<br>

Blanco Melo D, Gifford RJ, and P. Bieniasz
<b>(2018)</b>
<br>
Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L.
<br>
<i>Retrovirology</i>
<a href="https://retrovirology.biomedcentral.com/articles/10.1186/s12977-018-0416-3" target="_blank">[view]</a>
<br>
<br>

Dennis TPW, Flynn PJ, de Souza WM, Singer JB, Moreau CS, Wilson SJ, and RJ Gifford
<b>(2018)</b>
<br>
Insights into circovirus host range from the genomic fossil record.
<br>
<i>Journal of Virology</i>
<a href="http://jvi.asm.org/content/92/16/e00145-18.full" target="_blank">[view]</a>
<br>
<br>

Dennis TPW, de Souza WM, Marsile-Medun S, Singer JB, Wilson SJ, and RJ Gifford
<b>(2018)</b>
<br>
The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.
<br>
<i>Virus Research</i>
<a href="https://www.sciencedirect.com/science/article/pii/S0168170217309048" target="_blank">[view]</a>
<br>
<br>


Blanco-Melo D, Gifford RJ, and PD Bieniasz
<b>(2017)</b>
<br>
Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors.
<br>
<i>Elife</i>
<a href="https://elifesciences.org/articles/22519" target="_blank">[view]</a>
<br>
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</p>


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56 changes: 20 additions & 36 deletions website/user-guide/user-guide.html
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Expand Up @@ -32,16 +32,21 @@ <h2 class="project-tagline">Database-Integrated Genome Screening</h2>



<h2>
<a id="Contents" class="anchor" href="#Contents" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Contents</strong>
</h2>
<h1>
<a id="Title" class="anchor" href="#Contents" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>DIGS User Guide</strong>
</h1>
<hr>


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

<p>


<ol>
<li> <a href="#Setup"><b>Setting up for DIGS</b></a>
<li> <a href="#Setup"><b>Installation & Set-up</b></a>
<br>
<br>
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<a href="#extractSequences"><li> Extracting hit sequences and their flanks using the DIGS tool</li></a>
</ol>
</li>
<br>
<li> <a href="#investigationStructure"><b>Structure of a DIGS-based investigation</li></b></a>
<br>
<ol>
<a href="#runScreen"><li> Running an <i>in silico</i> screen</li></a>
<a href="#inspectResults"><li> Investigating screening results via a GUI SQL client</li></a>
<a href="#updateRefSeqsAndReassign"><li> Updating reference sequences and reclassifying results</li></a>
<a href="#addingSideData"><li> Incorporating linked data into a DIGS project</li></a>
<a href="#consolidate"><li> 'Consolidate': Merging hits in the DIGS results table into larger sequences.</li></a>
<a href="#extractSequences"><li> Extracting hit sequences and their flanks using the DIGS tool</li></a>
<a href="#screenStructure"><li> Overview of a DIGS-based investigation</li></a>
<a href="#explorationPhase"><li> Exploration phase</li></a>
<a href="#analysisPhase"><li> Analysis phase</li></a>
</ol>
</li>
</ol>
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<h2>
<a id="Setup" class="anchor" href="#Setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>1. Setting up for DIGS</strong>
<a id="Setup" class="anchor" href="#Setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>1. Installation & Set-up</strong>
</h2>
<hr>





<h3>
<a id="installSoftware" class="anchor" href="#environmentVariables" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>1.1. Software requirements</strong>
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<br>
<h2>
<a id="performingScreening" class="anchor" href="#performingScreening" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Part 2. Performing DIGS and working with project databases</strong>
<a id="performingScreening" class="anchor" href="#performingScreening" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>2. Performing DIGS and working with project databases</strong>
</h2>
<hr>



<h3>
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</p>

<br>

<h2>
<a id="Setup" class="anchor" href="#Setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>3. Structure of a DIGS-based investigation</strong>
<a id="screenStructure" class="anchor" href="#Setup" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>3. Structure of a DIGS-based investigation</strong>
</h2>
<hr>


<br>
<h3>
<a id="SearchStructure" class="anchor" href="#SearchStructure" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Overview</strong>
<a id="screenStructure" class="anchor" href="#SearchStructure" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>3.1 Overview</strong>
</h3>
<hr>

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<h3>
<a id="setUpAndRunScreen" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Exploration phase: Setting up and running an <i>in silico</i> screen</strong>
<a id="explorationPhase" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>3.2 Exploration phase: Setting up and running an <i>in silico</i> screen</strong>
</h3>
<hr>

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<br>
<h3>
<a id="analyseScreenOutput" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Analysis phase: Inspecting results and exporting data for comparative analysis</strong>
<a id="analysisPhase" class="anchor" href="#setUpAndRunScreen" aria-hidden="true"><span class="octicon octicon-link"></span></a><strong>Analysis phase: Inspecting results and exporting data for comparative analysis</strong>
</h3>
<hr>

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(some comparative analysis do not require an alignment, but most do).
</blockquote>




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