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<!DOCTYPE html>
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.tabcontent {
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</head>
<p>Welcome to CRESSdna.org</p>
<ul class="top-level-menu">
<li><a href="#" class="tablinks" onclick="openTab(event, 'Home')" id="defaultOpen">Home</a></li>
<li>
<a href="#">Taxonomy</a>
<ul class="second-level-menu">
<li><a href="#" class="tablinks" onclick="openTab(event, 'Circoviridae')">Circoviridae</a></li>
<li><a href="#" class="tablinks" onclick="openTab(event, 'Nanoviridae')">Nanoviridae</a></li>
<li><a href="#"><i>more on the way</i></a></li>
</ul>
</li>
<li>
<a href="#">Classifier</a>
<ul class="second-level-menu">
<li><a href="#" class="tablinks" onclick="openTab(event, 'Classifier')">Run the classifier</a></li>
<li><a href="#" class="tablinks" onclick="openTab(event, 'Results')" id="defaultOpen">Results</a></li>
</ul>
</li>
<li><a href="#" class="tablinks" onclick="openTab(event, 'Resources')">Resources</a></li>
<li><a href="#" class="tablinks" onclick="openTab(event, 'Contributers')">Contributers</a></li>
<li><a href="#" class="tablinks" onclick="openTab(event, 'Contact')">Contact</a></li>
</ul>
<div id="Home" class="tabcontent">
<h3>Home</h3>
<p>Part of the <a href='http://www.nsf.gov/pubs/2010/nsf10513/nsf10513.htm'>National Science Foundation's Assembling the Tree of Life</a>.</p>
<img src='nsf1.jpg' alt='Sponsored with a Grant from the National Science Foundation'>
</div>
<div id="Circoviridae" class="tabcontent">
<h3><i>Circoviridae</i></h3>
<p>
Many animal-infecting CRESS-DNA viruses are classified into the <a href="http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000871"><i>Circoviridae</i> family</a>. There are two genera within the group, the older <i>Circovirus</i> and the more recently codified <i>Cyclovirus</i>, but both are well represented. At least one disease of economic importance is associated with circovirus infections: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3652492/">post-weaning maturation wasting syndrome</a> in pigs (caused in part by porcine circovirus 2, which is now largely controlled through <a hfref="https://www.ncbi.nlm.nih.gov/pubmed/27769529">vaccination in commercial hog production</a>). However, several worldwide veterinary diseases are due to circoviruses, including <a href="https://en.wikipedia.org/wiki/Psittacine_beak_and_feather_disease">beak and feather disease</a> and <a href="https://www.ncbi.nlm.nih.gov/pubmed/28242782">fatal acute diarrhea</a> in dogs.
</p>
<figure>
<img class=scaled src="../DogCV.png", alt='missing' />
<figcaption><a href="https://wwwnc.cdc.gov/eid/article/19/4/12-1390-f2">Gastrointestinal system of dogs infected with dog circovirus</a> (DogCV) with hemorrhaging in stomach and intestines. CC-BY Li et al. 2013</figcaption>
</figure>
<figure>
<img class=scaled src="../PCV2.jpg", alt='missing' />
<figcaption><a href="https://virologyj.biomedcentral.com/articles/10.1186/1743-422X-8-291">Immune electron microscopy image of PCV2</a> (porcine circovirus 2) particles. CC-BY Guo et al. 2011</figcaption>
</figure>
<p>
While some of the environmental isolates assigned to <i>Circoviridae</i> have genomes over 3,000 and 4,000 bases, it also contains some of the smallest genomes of CRESS-DNA viruses – some well-studied circoviruses have genomes ~1700nt long, and circularized putative genomes from metagenomics studies can be even smaller. Most analyzed sequences have two ORFs: the replication-associated protein (Rep, also referred to as the replication initiator protein) and capsid protein (Cp or Cap), with some isolates having had a third ORF experimentally verified, and some sequences having many hypothetical ORFs called that have not yet been studied in the lab.
</p>
<p>
Both cycloviruses and circoviruses have non-enveloped, icosahedral virions of 15-25nm encapsidating their circular, ssDNA genomes, but while members of <i>Circovirus</i> are found infecting or associated with mammals, birds and fish, cycloviruses have been found infecting or associated with mammals, birds and insects. Sequences assigned to <i>Circovirus</i> have ambisense genomes, with the Rep gene in sense, sequences in Cyclovirus typically are ambisense in the opposite orientation (Rep gene in anti-sense).
</p>
<p>
A great <a href="http://jgv.microbiologyresearch.org/content/journal/jgv/10.1099/jgv.0.000871">primer</a> on <i>Circoviridae</i>
</p>
<p>
For more information about <i>Circovirus</i>:
<br>
<a href="https://talk.ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae/659/genus-circovirus">ICTV report</a> on circovirus
<br>
<a href="https://viralzone.expasy.org/118">ExPASy ViralZone summary of circovirus</a>
<br>
Type species: <i>Porcine circovirus</i> 1 (<a href="https://www.ncbi.nlm.nih.gov/nuccore/12280941">NC_001792.2</a>)
</p>
<p>
For more information about <i>Cyclovirus</i>:
<br>
<a href="https://talk.ictvonline.org/ictv-reports/ictv_online_report/ssdna-viruses/w/circoviridae/660/genus-cyclovirus">ICTV report</a> on cyclovirus
<br>
<a href="https://viralzone.expasy.org/7296">ExPASy ViralZone summary of cyclovirus</a>
<br>
Type species: <i>Human-associated cyclovirus 8</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/KF031466">KF031466</a>)
</div>
<div id="Nanoviridae" class="tabcontent">
<h3><i>Nanoviridae</i></h3>
<p>
The plant infecting CRESS-DNA viruses with more than two genomic segments belong in the family <a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae"><i>Nanoviridae</i></a>,
which includes the genera <i>Babuvirus</i> and <i>Nanovirus</i>. One of the most economically important species in the family <i>Nanoviridae</i> is Banana bunchy top virus (BBTV), the type species of babuvirus. BBTV causes
<a href="http://www.promusa.org/Bunchy+top">banana bunchy top disease</a>, which is common in banana growing areas such as Southeast Asia, the South Pacific, India and Africa. This virus is transmitted by the banana aphid and causes
<a href="http://www.musarama.org/en/image/bunchy-top-symptom-81.html">plant crumpling, shrinking and chlorosis</a>, which may develop into necrosis.
<br>
<figure>
<img class=scaled src="../bbv.jpg", alt='missing', width="512", height="384"/>
<figcaption>Banana bunchy top, caused by Banana bunchy top virus (BBTV). CC-BY Scott Nelson 2014.</figcaption>
</figure>
<p>
Viruses in the family Nanoviridae have <a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">multipartite genomes</a>
consisting of 6 to 8 ~1000 nucleotide segments of circular ssDNA. Five of these DNA components are shared between babuviruses and nanoviruses.
<a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/150/nanoviridae-figures">(DNA-R, -N, -S, -C and –M)</a>.
Nanoviruses infect <a href="http://theseedsite.co.uk/monocots2.html">dicots</a>, have 8 genomic DNAs and may include three other DNA components with functions
that have yet to be determined (DNA-U1, -U2 and –U4). Babuviruses infect <a href="http://theseedsite.co.uk/monocots2.html">monocots</a>, have 6 genomic DNAs
and may include another DNA component with an unknown function (DNA-U4). Each of these components encode a single ORF that is transcribed in one direction,
though a second putative ORF has been identified on one segment of BBTV (DNA-R). The virions of these viruses are non-enveloped, sized 17-20nm in diameter
and have one CP (coat protein). Additional DNA segments (alphasatellites) are also associated with many viruses in the family and can alter disease symptoms.
</p>
<p>
For more information about Nanovirus:
<br>
<a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">ICTV report</a> on nanovirus.
<br>
<a href="https://viralzone.expasy.org/565?outline=all_by_species">ExPASy ViralZone summary of nanovirus</a>
<br>
Type Species: <i>Subterranean clover stunt virus</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_003818.1">NC_003818.1</a>)
</p>
<p>
For more information about Babuvirus:
<br>
<a href="https://talk.ictvonline.org/ictv-reports/ictv_9th_report/ssdna-viruses-2011/w/ssdna_viruses/149/nanoviridae">ICTV report</a> on babuvirus.
<br>
<a href="https://viralzone.expasy.org/564?outline=all_by_species">ExPASy ViralZone summary of babuvirus</a>
<br>
Type Species: <i>Banana bunchy top virus</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_003479.1">NC_003479.1</a>)
</p>
</div>
<div id="Classifier" class="tabcontent">
<h3>Classifier</h3>
<form action="./bin/classifier2.py" method="post"><br>
<textarea rows="4" cols="50" name="fasta" input type="submit">>Demo
MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI</textarea>
<br>
<input type="reset">
<input type="submit">
</form>
<p>
<ul>
<li>This classifier requires Rep protein sequence to be:</li>
<ul>
<li>Complete</li>
<li>Unaligned</li>
<li>in FASTA format</li>
</ul>
<p>And has been trained on the following Genera:</p>
<li>Circoviridae</li>
<ul>
<li>Circovirus</li>
<li>Cyclovirus</li>
</ul>
<li>Nanoviridae</li>
<ul>
<li>Babuvirus</li>
<li>Nanovirus</li>
</ul>
<li>Genomoviridae</li>
<ul>
<li>Gemycircularvirus</li>
<li>Gemygorvirus</li>
<li>Gemykibivirus</li>
<li>Gemykolovirus</li>
<li>Gemykrogvirus</li>
<li><strike>Gemyvongvirus</strike></li>
</ul>
<li>Geminiviridae</li>
<ul>
<li>Becurtovirus</li>
<li>Begomovirus</li>
<li>Capulavirus</li>
<li>Curtovirus</li>
<li>Eragrovirus</li>
<li>Grablovirus</li>
<li>Mastrevirus</li>
<li>Turncurtovirus</li>
</ul>
<li>Smacoviridae</li>
<ul>
<li>Huchismacovirus</li>
<li>Porprismacovirus</li>
</ul>
<li>Bacilladnaviridae</li>
<ul>
<li>Protobacilladnavirus</li>
</ul>
</ul> </p>
</div>
<div id="Resources" class="tabcontent">
<h3>Resources</h3>
<p><a href="https://github.com/elavington/CRESS-DNA-virus-classification/blob/master/ProtTest_withCRESS.zip">ProtTest3 with CRESS DNA virus model</a></p>
<p>ProtTest3 with a CRESS DNA virus based substitution matrix developed by Lele Zhao.</p>
</div>
<div id="Contributers" class="tabcontent">
<h3>Contributers</h3>
<p>This site is under construction</p>
<p>Please be patient while we tidy up a bit!</p>
</div>
<div id="Contact" class="tabcontent">
<h3>Contact</h3>
<p>This site is under construction</p>
<p>Please be patient while we tidy up a bit!</p>
</div>
<div id="Results" class="tabcontent">
<h3>Results</h3>
<p>Results from Taxonomy prediction</p>
</div>
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