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7 results for “virus taxonomy”
MMseqs2 virus protein database with ICTV taxonomy
<p>MMseqs2 virus protein database decorated with ICTV taxonomy. Proteins originally retrieved from NCBI NR in 2025-02-08.</p> <p>Steps for reproduction can be found at https://github.com/apcamargo/ictv-mmseqs2-protein-database</p>
Fig 2 in Four principles to establish a universal virus taxonomy
Fig 2. Structure-based dendrogram of capsid proteins of members of the kingdom Bamfordvirae. Structure-based phylogenetic tree inferred from major capsid protein (MCP) structures of the members of the kingdom Bamfordvirae in the Varidnaviria realm. Members of Bamfordvirae encode a vertical double-jelly roll fold MCP, which is the hallmark protein of this group of viruses. Next to each MCP structure are the virus name (top), the phylum (middle), and family (bottom), with "Faustovirus" not yet officially classified and Finnlakeviridae not yet assigned to any higher taxon. The evolutionary distances across the depicted members of the originally called PRD1-adenovirus viral lineage [67] were calculated with the Homologous Structure Finder software [50] and depicted with PHYLIP (https://evolution.genetics.washington.edu/phylip.html); the evolutionary distances are shown next to each branch. The protein data bank identifiers (PDBid) for the structures are as follows: PRD1: PDBid 1HX6; PBCV-1: 1M3Y; adenovirus: 1P2Z; STIV: 2BBD; Vaccinia D13: 2YGB; Sputnik: 3J26; Faustovirus: 5J7O; FLiP: 5OAC; ASFV p72: 6KU9; PM2: 2W0C. Adapted from [62]. https://doi.org/10.1371/journal.pbio.3001922.g002
Fig 1 in Four principles to establish a universal virus taxonomy
Fig 1. Ranks used in virus taxonomy. Schematic depiction of the 15-rank taxonomic framework used by the ICTV. It includes the methodologies that may be used to determine virus evolutionary relationships and make assignments at each rank. The pyramid shape indicates that the number of taxa increases from the top rank (realm) to the most basal rank (species, Sp.). The names of the 15 ranks are shown on the left of the pyramid, and the methodologies are on the right (AAS, amino acid sequence similarity; NS, nucleotide sequence similarity). The pyramid includes a hypothetical example of the taxonomy of a realm, indicating the number of taxa at each rank (filled circles). The phenotypic properties of classified viruses that may inform rank placements are depicted below the pyramid. https://doi.org/10.1371/journal.pbio.3001922.g001
Prospects for a sequence-based taxonomy of influenza A virus subtypes
<p>This dataset comprises the multiple sequence alignments (*.fasta) and maximum likelihood phylogenies (Newick tree strings, *.nwk) for all available protein sequences corresponding to the eight genome segments of influenza A virus from the NCBI Genbank database. </p> <p>Each sequence is labelled with the Genbank accession number (e.g., "CY103884"), WHO strain identifier ("A/little yellow-shouldered bat/Guatemala/164/2009"), subtype label ("H17N10"), host species ("Sturnira lilium; gender M"), sampling location ("Guatemala: El Jobo"), and sample collection date ("May-2009"). These fields are separated by underscore characters.</p> <p>These data are provided under a Creative Commons license in support of a manuscript in progress, "Prospects for a sequence-based taxonomy of influenza A virus subtypes".</p>
ICTV Virus Taxonomy (ICTV)
From: [TRAM-532](<p></p>https://eol-jira.bibalex.org/browse/TRAM-532)<p></p>Data sets for the assembly of the EOL dynamic hierarchy.
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively. in The species Severe acute respiratory syndromerelated coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
History of coronavirus naming during the three zoonotic outbreaks in relation to virus taxonomy and diseases caused by these viruses. According to the current international classification of diseases49, MERS and SARS are classified as 1D64 and 1D65, respectively.
Fig 3 in Four principles to establish a universal virus taxonomy
Fig 3. Examples of incompatibilities between species assignments and phylogenetic groupings. (A) Genetic relationships of HIV-1 (red dots) with simian immunodeficiency viruses infecting chimpanzees (gray dots) and gorillas (black dots). HIV-1 strains are polyphyletic and cannot be assigned to a single species taxon without incorporating nonhuman viruses within the definition. (B) Genetic relationships of louping ill virus (LIV) with tick-borne encephalitis virus (TBEV) strains isolated in Europe and Asia, with the principal groups labeled. Although LIV (red dots) is assigned to the species Louping ill virus, it lies within the phylogenetic tree created by strains of TBEV that all belong to the species Tick-borne encephalitis virus. The current assignment of LIV as a species therefore logically prevents strains of TBEV being assigned into a single species if species were to remain monophyletic. Trees were constructed from maximum composite likelihood distances between nucleotide sequences of (A) the pol gene of HIV-1/SIV and (B) the complete coding sequence of TBEV and LIV. To investigate the robustness of branches, nucleotide positions were bootstrap resampled 100 times as implemented in the MEGA7 program [91]; branches with 70% or greater support are labeled. The HIV-1/SIV tree was rooted using the HIV-2 sequence, M31113; the TBEV/LIV tree was rooted using the closely related Omsk haemorrhagic fever virus sequence, AY193805. Both trees have been annotated with a scale bar indicating substitutions per site. https://doi.org/10.1371/journal.pbio.3001922.g003
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.