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Virus Pathogen Resource (Vipr) September 2018 New Features in Vipr Virus Pathogen Resource (ViPR) September 2018 New Features in ViPR New virus portals for Phenuiviridae For example, certain nodes/subtrees can Monthly Webinars and Peribunyaviridae be either too closely or too distantly related To help you use IRD/ViPR more to be informative. The new version of effectively, we are hosting monthly After the reclassification of the Bunyaviridae Archaeopteryx.js therefor allows deleting webinars. family as Bunyavirales order by the nodes/subtrees directly from the tree so International Committee on Taxonomy that users do not need to recompute the • November 6, 2018, 9-10 Pacific: of Viruses (ICTV), the ViPR team has been tree in order to remove certain nodes. Host factor data analysis continuously building new virus family • December 4, 2018, 9-10 Pacific: collections to reflect the taxonomic changes. • Dynamic update of figure legends: After Sequence Feature Variant Type In this release, new Phenuiviridae and a tree display is limited to a subtree or analysis Peribunyaviridae portals are available within nodes have been deleted from a tree, the the ViPR site. Each virus family home page figure legends such as label colors will be Please register here. allows you to easily search, retrieve, and dynamically updated to reflect the data analyze virus data for the selected family. being displayed. News & Events • access integrated data: genomes/ • October 8-11, 2018: 25th Please see figure below for an example. segments, proteins, immune epitopes and International Symposium on Hepatitis 3D protein structures. C Virus and Related Viruses, Dublin, Ireland. Oral presentation. • use a suite of analysis tools: multiple 10/1/2018 sequenceVirus Pathogen alignment, Database and Analysis Resource (VphylogeneticiPR) - Genome database with visualization and analysistree tools • January 14-17, 2019: Bioinformatics constructionLoading andVirus Pathogen visualization, Database and AnalysisAbout Resource Us Community (ViPR)... Announcementsmetadata-Links Resources Support training workshop, Qatar University, driven comparative analysis, sequence Doha, Qatar Search Analyze Save to Workbench Searchvariation our comprehensive database analysis,for: Analyze data online:BLAST, shortUse yourpeptide workbench to: Sequences & strains Sequence Alignment Store and share data Immune epitopes Phylogenetic Tree Combine working sets 3Dsearch, protein structures PCR primerSequence Variation design, (SNP) genomeIntegrate your data with ViPR data Host Factor Data Metadata­driven Comparative Analysis Store and share analyses Antiviralannotation, Drugs etc.BLAST Custom search alert Sequence Search API Browse All Search Types Browse All Tools • Supported store Programs and share data via your Workbench The ViPR sequence search application Click on a supported program of interest to go to program description page. programming interface (API) has been NIAID Functional Genomics NIAID Systems Biology Virus Families continuously improved. The newest version 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 Single­Stranded Positive­Sense RNA Single­Stranded Negative­Sense RNA Double­Stranded RNA Double­Stranded DNA of the API now supports additional sequence Caliciviridae Picornaviridae Arenaviridae Paramyxoviridae Reoviridae Herpesviridae New! search fields and more sequence-associated Coronaviridae Togaviridae Filoviridae Peribunyaviridae Poxviridae New! New! metadata fields available for retrieval. Flaviviridae Hantaviridae Phenuiviridae New! Hepeviridae Nairoviridae Rhabdoviridae Newly supported search fields include: Featured Viruses Virus News Click on a featured virus of interest to go to virus­specific home page. Updated 31 August 2018 ViPR has added two new sites, for Nairoviridae and Hantaviridae Dengue virus Ebolavirus Enterovirus Hepatitis C virus IRD/ViPR Monthly Webinars: September 11, • ViPR-annotated complete genome 2018 to December 4, 2018 Lassa Virus Zika Virus July 27, 2018 ­ World map of April­June 2018 ProMED’s infectious disease surveillance reports. Highlights July 3, 2018 ­ A new machine learning method • GenBank-annotated complete sequence has been reported in Nature to predict potential hosts of Influenza, Rhabdovirus and Coronavirus species. A portion of thePhylogenetic ViPR Trees homepage Mayshowing 2, 2018 ­ Peck and Lauring have ViPR uses PhyML (Guindon and Gascuel, 2003) and comprehensively estimated mutation rates of 25 An HCV genome tree visualized in the virus species. offers multiple evolutionary models to infer phylogenies. Update on the Nipah Virus outbreak in Kerala, • ViPR-curated continent the new PhenuiviridaeDecoration options let you color treeand leaves by metadata. PeribunyaviridaeIndia. Export image and legend, or download trees as Newick or In early May the Nigerian Center for Disease PhyloXml files for other viewing software. Control and WHO reported that the Lassa Fever Archaeopteryx.js tree viewer. outbreak has been contained, although Key Highlights: continuing vigilance was necessary. From January 1 to June 24 2018 444 confirmed cases families Quick Tree produces an accurate topology for > • ViPR-annotated Rotavirus G/P genotype including 111 deaths had been reported. Click 1,000 sequences. Custom Tree lets you choose an here for the latest outbreak news. ViPR Tree is midpoint rooted (clicking M in the evolutionary model and parameter values. supports research on Lassa virus, with various types of data and bioinformatics analysis tools. ModelCompare (Custom Tree) suggests an Start Analysis Yuan, et al. report that a single S139N mutation evolutionary model to best fit the data. on the polyprotein of Zika virus contributes to Specify metadata for the leaves (strain name, etc.) fetal microcephaly. See the ViPR Analysis Tools panel). Sequence labels are colored Tutorial Newly supported metadata fields for retrieval Report on finding Zika strains carrying this include: https://www.viprbrc.org/brc/home.spg?decorator=vipr 1/2 by ViPR-annotated genotype (choosing Enhanced Archaeopteryx.js Tree Subtype/Genotype in the Label Color • ViPR-curated continent Viewer menu in the Visualizations panel). Left- Instructions, along with examples, are The powerful Archaeopteryx.js tree viewer clicking a node displays a function menu. described at Support > IRD/ViPR APIs. has been further enhanced with the following From this menu, users can click Delete new features: Subtree to remove the subtree rooted at the clicked node. The figure legend will be The September 2018 release • Deletion of subtrees/external nodes: dynamically updated based on the data in of ViPR is now available, visit During phylogenetic analysis, it is the modified tree. The modified tree can www.viprbrc.org sometimes useful to remove certain nodes/ be downloaded in image (PNG, SVG) or subtrees after a tree has been generated. tree formats (phyloXML, Newick). Questions? Problems? Suggestions? Click Here.
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