Virus Pathogen Resource (ViPR) March 2019 New Features in ViPR

New Genome Annotation Tool New RNA Structure Data VIGOR4, a new genome annotation tool is In collaboration with the NIAID-funded Loading Virus Pathogen Database and AnalysisAbout Resource Us Community (ViPR)... Announcements Links Resources Support now available on the Zika virus portal. VIGOR4 Orfeome project, we have released new RNA News & Events (Viral Genome ORF Reader) is developed by structure data for MERS-CoV on the ViPR • June 9-13, 2019: Positive Strand J. Craig Venter Institute. VIGOR 4 predicts site. This new dataset is generated as part RNA Viruses, Killarney, Ireland. Oral protein sequences encoded in a viral of the effort to identify, characterize and presentation. genomes by sequences similarity searching then determine the role of uncharacterized against curated viral protein databases. viral genesSearch that may function to auto- Analyze• July 21-25, 2019: Annual Conference Save to Workbench regulate virus replication efficiency and host In the next few releases, we will enhance the Search our comprehensive database for: Analyzeon Intelligent data online: Systems for Molecular Use your workbench to: responses. The structure data is predicted Biology, Basel, Switzerland. current VIGOR4 implementation and make it Sequences & strains Sequence Alignment Store and share data available for other virus familes. using SHAPE chemical reactivity data (PMID: 22475022Immune). epitopes • AugustPhylogenetic 4-9, T2019:ree 24th International Combine working sets 3D protein structures BioinformaticsSequence Variation Workshop (SNP) on Virus Integrate your data with ViPR data Loading Virus Pathogen Database and Analysis Resource (ViPR)... To access the new RNA structure data, go to Zika Virus Host Factor Data EvolutionMetadata­driven and MolecularComparative Epidemiology Analysis Store and share analyses About Us Community Announcements Links Resources Support ViPR homepage > NIAID Functional Genomics SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HELP [email protected] (VEME), Hong Kong ViPR Home Zika Virus Home VIGOR (Viral Genome ORF Reader) Annotation Antiviral Drugs BLAST Custom search alert Genome Annotation (VIGOR4) > ORFEOME Project > Middle East Respiratory VIGOR4 (Viral Genome ORF Reader) is developed by J. Craig Venter Institute. VIGOR 4 predicts protein sequences encoded in a viral genomes by sequences similarity Plasmid Data searching against curated viral protein databases. Syndrome (MERS) Coronavirus. The open­source code for the custom version of VIGOR4 can be found here .

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ANALYSIS NAME SELECT A VIRUS REFERENCE DATABASE * Coronaviridae Annotations: 100 bp from KJ614529:9,951..10,050 Browser Select Tracks Snapshots Custom Tracks Preferences Publications

Search INPUT SEQUENCES * Vigor4 supports annotation of the above listed virus. Landmark or Region: Analyze my custom sequences only. For other virus, please use the GATU Annotator. Upload a file containing my sequences in FASTA format. SET PARAMETERS Examples: KJ614529:1..134, KJ614529. Paste sequences in FASTA format. NCBI locus tag assigned to BioProject (Optional) Data Source Scroll/Zoom: Flip • Brown DM, Zhang Y, Scheuermann Analyze my custom sequences and associated metadata with Coronaviridae Annotations Do NOT use locus tag ViPR sequences. Overview Supported Programs Use Locus Tag RH. Epidemiology and Evolution of Region Clear Run Click on a supported program of interest to go to program description page. Details Circulating Non-polio Enteroviruses 20 bp Release Date: Mar 27, 2019 This system is provided for authorized users only. Anyone using this system expressly consents to monitoring while using the system. Improper use of this system may be referred to law enforcement officials. Protein-coding genes Using Sequence-Based Analysis. This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S. Department of Veterans Pfam domains Affairs, Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics. ViPR-generated Mature Peptide Virology, submitted. RNA Structure1 (ENERGY: -13543.5NIAID kcal/mol) Functional Genomics NIAID Systems Biology

RNA Structure2 (ENERGY: -13542.5 kcal/mol) The VIGOR4 tool is now available on the Zika RNA Structure3 (ENERGY: -13541.6 kcal/mol) portal (ViPR homepage > Zika Virus > Analyze SHAPE Reactivity Data SHAPE Data Virus Families & Visualize > VIGOR4 Genome Annotator). Loading Virus Pathogen Database and Analysis Resource (ViPR)... Click on icon of family or species of interest. Click here to to view all families and species in list format. Don't know family of species? Provide species name

Flaviviridae RNA sequence About Us Community Announcements Links Resources Support

SEARCH DATA ANALYZE & VISUALIZE WORKBENCH VIRUS FAMILIES HELP [email protected]

ViPR Home Flaviviridae Home My Workbench Analysis (VIGORANNOTATOR4) Release Date: Mar 27, 2019 VIGOR Genome Annotation Report This system is provided for authorized users only. AnyoneSingle­Stranded using this system expressly consents to monitoring whilePositive­Sense using the system. Improper use of this system may RNA be referred to law Single­Stranded Negative­Sense RNA Double­Stranded RNA Double­Stranded DNA enforcement officials. Save Analysis Download ▼ This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between Northrop Grumman Health IT, J. Craig Venter Institute, and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library, Wellcome Images, U.S. Department of Veterans Your analysis generated results from 1 input sequence(s). Affairs, Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics. Gene Identifier Start Stop Gene Product Name Referenece Peptide Length Reference Length %Identity %Similarity %Coverage The genome annotations of MERS- New! Haiti.1 108 10379 genome polyprotein KU647676 3423 3423 99.80 99.91 100.00 Haiti.1.1 474 752 protein pr KU647676_pr 93 93 100.00 100.00 100.00 Caliciviridae Hepeviridae Rhabdoviridae Reoviridae Herpesviridae Haiti.1.2 753 977 small envelope protein M EU545988_M 75 75 100.00 100.00 100.00 Coronavirus Jordan-N3/2012 (KJ614529) are Bunyavirales Haiti.1.3 978 2489 envelope protein E KU647676_E 504 504 100.00 100.00 100.00 Haiti.1.4 2490 3545 nonstructural protein NS1 KU647676_NS1 352 352 99.43 99.72 100.00 Haiti.1.5 3546 4223 nonstructural protein NS2A KU744693_NS2A 226 226 100.00 100.00 100.00 shown in GBrowse on ViPR. Three predicted Haiti.1.6 4224 4613 nonstructural protein NS2B EU545988_NS2B 130 130 100.00 100.00 100.00 Haiti.1.7 4614 6464 nonstructural protein NS3 KU647676_NS3 617 617 100.00 100.00 100.00 RNA structures with the lowest-energies and Haiti.1.8 6465 6845 nonstructural protein NS4A KU647676_NS4A 127 127 100.00 100.00 100.00 Coronaviridae Picornaviridae Filoviridae Poxviridae Haiti.1.9 6846 6914 protein 2K KF383118_2K 23 23 100.00 100.00 100.00 Haiti.1.10 6915 7667 nonstructural protein NS4B KU647676_NS4B 251 251 100.00 100.00 100.00 SHAPE reactivity data are shown along with Haiti.1.11 7668 10376 RNA­dependent RNA polymerase NS5 EU545988_NS5 903 903 99.56 100.00 100.00 gene, protein and domain annotations of Release Date: Mar 27, 2019 Flaviviridae Togaviridae Paramyxoviridae This system is provided for authorized users only. Anyone using this system expressly consents to monitoring while using the system. Improper use of this system may be referred to law enforcement officials. This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272201400028C and is a collaboration between Northrop the genome. The RNA structure data can be VIGORGrumman Health IT, J. Craig annotationVenter Institute, and Vecna Technologies. Virus imagesresults courtesy of CDC Public ofHealth Image a Library Zika, Wellcome Images virus, U.S. Department of Veterans Affairs, Science of the Invisible and ViralZone, Swiss Institute of Bioinformatics. downloaded to a local computer. genome. Mature peptide sequences are also The new Bunyavirales order now contains six Featured Viruses Virus News predicted and available for download. virus families including Arenaviridae. Click on a featured virus of interest to go to virus­specific home page. Updated 25 February 2019 Arenaviridae Relocation Lancet reviews the resurgence of vector­borne disease in the midst of Venezuela’s political and Following the ICTV recommendations of re- Virus-BRC Github Repositories humanitarian crisis. classifying ArenaviridaeDengue virus into the Bunyavirales,Ebolavirus Enterovirus Hepatitis C virus Following ICTV recommendations, the ViPR Source code for tools developed or Arenaviridae site is now accessed via the new the Arenaviridae family of the ViPR site has customized by the Virus-BRC team is now Bunyavirales icon. ViPR sites for Nairoviridae, Hantaviridae, The March 2019 release been moved intoLassa the V irusBunyavirales Zikaorder. Virus of ViPR is now available, visit available on the Virus-BRC Github. We will Peribunyaviridae, Phasmaviridae, and To access Arenaviridae, ViPR homepage > continue to share source code for new and Phenuiviridae via the Bunyavirales icon. www.viprbrc.org ViPR also offers API retrieval of sequence and BunyaviralesHighlights > Choose Arenaviridae from the existing tools, over upcoming releases of IRD associated metadata from all families in the Bunyavirales order, including: Fimoviridae, etc. dropdown list > Arenaviridae. and ViPR. Click here for API instructions and examples. Nov 2, 2018 ­ Babayan, et al. report a machine Mature Peptides learning method for using genomic sequence of Mature viral protein products resulting from protease­ and RNA viruses to predict reservoir host, and the existence and identity of arthropod vectors. self­cleavage of the polyprotein are displayed according to

Questions? Problems? Suggestions? their location in the genome and the polyprotein. Previous Scientific Reports Click Here Key Highlights: Visualize viral mature peptides Connect with Us Display location of mature peptide

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