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<body>
<p>Welcome to CRESSdna.org</p>
<div class="tab">
<button class="tablinks" onclick="openTab(event, 'Home')" id="defaultOpen"class>Home</button>
<button class="tablinks" onclick="openTab(event, 'Circoviridae')"><i>Circoviridae</i></button>
<button class="tablinks" onclick="openTab(event, 'Classifier')">Classifier</button>
<button class="tablinks" onclick="openTab(event, 'Contact')">Contact</button>
<button class="tablinks" onclick="openTab(event, 'Results')">Results</button>
</div>
<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>
<br>
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-senese).
</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>
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>
Type species: <i>Human-associated cyclovirus 8</i> (<a href="https://www.ncbi.nlm.nih.gov/nuccore/KF031466">KF031466</a>)
</div>
<div id="Classifier" class="tabcontent">
<h3>Classifier</h3>
<form action="./bin/classifier.py" method="post"><br>
<textarea rows="4" cols="50" name="fasta" input type="submit">>Demo
MPSKKSGPQPHKRWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTAHLQGFANFAKKQTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAYFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTINGGTRRPI</textarea>
<br>
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<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>Gemyvongvirus</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>Smacovirus</li>
</ul> </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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