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@@== ░ The Platinum Age of Virus░Discovery ░ ==@@
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Each living species can be infected by distinct constellations of viruses.
Here, we collectively interrogate how viruses and virus-like agents distribute
across life on Earth, through the re-analysis of 40+ million biological samples
which have undergone high-throughput DNA/RNA sequencing.
~=== It's dangerous to go alone! Take these. ===~ [click to expand]
Index of the software tutorials, web tools and analysis.
- Infernal # Search RNA Structures
- mFold # Secondary Fold DNA/RNA
- ORFfinder # Open Reading Frame calculator
- OpenVirome # RdRp palmprint graph tool
- RNAfold # Secondary Fold DNA/RNA
- sixpack # Six-frame translation calculator
- AlphaFold3 (A) | Version. (B) # Protein Structure prediction
- IUPred2A # Dirordered Sequence prediction
- muscle # Multiple Sequence Alignment (MSA)
- PepInfo # Protein summary statistics
- Phyre # Protein Structure prediction (old)
- ProteInfer # Protein Function predictor
- BLAST - BLASTp # Protein Search in Protein Database
- BLAST - BLASTx # Translated Nucleotide Search in Protein Database
- BLAST - tBLASTn # Protein Search Search in Nucleotide Database
- FoldSeek # Protein Structure Search
- HHpred # HMM Model Search Tools
- InterProScan # InterPro HMM Model Search
- MGnify_search # MGnify assemblage search
- PebbleScout # Nucleotide kmer search (big)
- MetaGraph # Nucleotide kmer search (bigger)
- Logan-Search # Nucleotide kmer search (Biggest)
- BLAST - tBLASTn for Virology # Find your viral contig in SRA
- Serratus Secret Wiki # Discover new viruses on the Serratus platform
- palmID # RdRp palmprint search tool
- iqtree # Generate phylogenetic tree from MSA
- MyDomains # Draws linear protein domain figure
- ChimeraX <VID> # Protein structure visualization with R interface
- PyMol # Protein structure visualization
Legend
- <99%> Exceptional Project
- <VID> Video Link
An index of the Virus Discovery Reports.
Mitoviriridae
- Agricolae Amicus (Mitovirus) <VID>
- Antagonascensor sororminor & sorormajor (Mitovirus) <VID> <99%>
- Fungicola clarireediae (Mitovirus) <VID> <99%>
- Golovinomyces furtivus (Mitovirus)
Narnaviridae
- Dulcivirus diffusus (Narnavirus) <VID>
- Insessor salmoscalpicī (Narnavirus) <VID>
- Narlivirus entericus (Narnavirus)
- Narnavirus nederspoliare (Narnavirus)
- Narnavirus porcinus (Narnavirus)
- Narnavirus subdolus (Narnavirus) <VID>
- Pax mycesfermentum (Narnavirus) <VID>
- Puccinia triticum (Narnavirus) <VID>
- Scandoremscalaria caecilius (Narnavirus) <VID>
- Novus bilinguis (Narnavirus)
- Glossinamyces chrysopsiformis (Narnavirus) <VID>
Partitiviridae
- Alphapartitivirus viator (Partitivirus) <VID>
- Durnavirus ambigiformis (Partitivirus) <VID>
- Fraterculapartitivirus comitans (Partitivirus) <VID>
- Mysticeovirus mutabilis.md (Partitivirus) <VID>
- Partitivirus sutilisdentis (Partitiviruse) <VID>
- Partitivirus rumenrex (Partitivirus) <VID>
Totiviridae
- Contaminivirus ubique (Totivirus) <VID>
- Diatototivirus sanguinis (Totivirus) <VID>
- Ovismusculus totivirae_desc (Totivirus) <VID>
- Sarcototivirus pseudocauda (Totivirus) <VID>
- Totivirus celatus (Totivirus)
- Sobemovirus hospes
An index of the Obelisk Discovery Reports.
- Aenigmovirus labrynthii
- Anas amicus
- Arcana rumenalis
- Clostridiae-associata centralis
- Gladius clandestinus
- Lineari obscurus
- Murinavoid maximus
- Mammalia ventremi
- Obeliscus aquidurentis
- Obeliscus faecalis
- Obeliscus porcinus <99%>
- Obeliscus replicandii <99%>
- Obeliskvirus respiratorius
- Obeliscus suslichen
- Obelisk 371
- Scrofobelisk intestinali
An index of the Virus Discovery Reports.
- Apiovirus anomala (Rhabdovirus)
- Arbovirus_chinensis (Orthomyxovirus)
- Blumevirus macaceinfi
- Black Queen Cell Virus (Picornavirus)
- Cripavirus inexspectatus (Dicistrovirus)
- Hemileia pugnator (Mitovirus) <99%>
- Hemiptinidovirus metis (Nidovirus)
- Hespivirus rivalense (Negevirus) <99%>
- Locarnavirus Nudiformis (Marnavirus)
- Orthocurvulavirus phantasma
- Posasimilis intestivirus (Posavirus)
- Pupavirus apiscarab (Narnavirus) <99%>
- Red Mite Associated Hypovirus 1
- Sedimentum occultus (Picornavirus)
- Thogotovirus_aidenensis (Orthomyxovirus)
- Totivirus Arthropodamyoti
- Trojan Patchwork Virus (Virga-like Virus)
- Vermisvirus culicis (Negevirus)
- Virusus intricatus trichomonadis (Totivirus)
- Add your Virus Report here ...
⦿ VIRUSxDISCVRY
├── template/ # Repository Template Files ======================
│ └─── toolTemplate.md # Template Markdown for the "Tool Tutorial",
│ │ # rename to tools/<toolname>.md
│ │
│ └─── virTemplate.md # Template Markdown for the "Virus Discovery
│ # Assignment", rename to virus/<virusname>.md
│
│
├── tools/ # Virus Discovery Tools Tutorials ================
│ │
│ └─── <toolname>.md # Upload your completed tutorial into this folder
│ │
│ └─── serratusexplorer.md # Example Tutorial for using Serratus.io Explorer
│ │
│ └─── img/<toolname>/ # For each <toolname>, supporting data or image
│ # files are in a seperate directory
│
│
├── virus/ # Virus Discovery Reports ========================
│ │
│ └─── <virusname>.md # Upload your completed virus discovery report
│ │ # into this folder
│ └─── img/<virusname>/ # For each <virusname>, supporting data or image
│ │ # files are kept in their own directory named
│ │ # after the virus
│ └─── vid/<virusname>/ # For each <virusname>, video descriptions
│ # for project YT channel
|
├── data/ # Example Data ==================================
│ │
│ └─── # Initial datasets for starting the project from
| # the 2023 RNA Virus Assignment. Allows for the
| # modules to be completed as a self-contained
| # tutorial / individual study project.
| # (Recommended) Instead of using these data,
| # select a random palmprint (palmDB) or
| # a library of specific interest (serratus.io)
| # as your initial seed.
│
├── README.md # Project README
├── LICENSE # AGPL 3.0 / cc0
├── vx.Rmd # Instructions for VIRUSxDISCVRY Project
├── lab2.Rmd # Instructions for Lab/Tutorial 2
├── lab3.Rmd # Instructions for Lab/Tutorial 3
│
⦿