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Journal Article
MoPSeq-DB: a user-friendly web application for genomic data management and analysis of marine mollusc pathogens Open Access
Database, Volume 2025, 2025, baaf080, https://doi.org/10.1093/database/baaf080
Published: 26 November 2025
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Summary of genome sequences and mutations in human coronaviruses. (A) Numbe... Open Access
Published: 26 November 2025
Figure 2.
Summary of genome sequences and mutations in human coronaviruses. (A) Number of genome sequences available for seven human coronaviruses. (B) Summary of mutation counts in the SARS-CoV-2 genome.
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General organization MoPSeq-DB. Each genome is stored in a dedicated storag... Open Access
Published: 26 November 2025
Figure 1.
General organization MoPSeq-DB. Each genome is stored in a dedicated storage directory, which contains the assembly file (.fasta), the annotations file (.gff), and detected variations file (.vcf) directly on disk. Simultaneously, all associated metadata is stored in a PostgreSQL database.
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MoPSeq-DB dataset structure. The data repository consists of subfolders cor... Open Access
Published: 26 November 2025
Figure 2.
MoPSeq-DB dataset structure. The data repository consists of subfolders corresponding to the pathogens listed in the database, categorized by their attribute ‘Pathogen’ attribute. For each pathogen, the repository contains four main folders (‘fasta’, ‘gff’, ‘phylo’, and ‘vcf’) to store different typ
Journal Article
HCoVDB: a comprehensive database encompassing viral genomes, drug targets, and therapeutics of human coronaviruses Open Access
Database, Volume 2025, 2025, baaf079, https://doi.org/10.1093/database/baaf079
Published: 26 November 2025
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The framework of the HCoVDB database. This database comprises three core co... Open Access
Published: 26 November 2025
Figure 1.
The framework of the HCoVDB database. This database comprises three core components: (1) genomic-level annotations, (2) target protein–compound interactions, and (3) antiviral activity data of small molecules.
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Screenshot illustrating an example of genome exploration in the HCoVDB data... Open Access
Published: 26 November 2025
Figure 3.
Screenshot illustrating an example of genome exploration in the HCoVDB database. (A) A detailed list of sources and basic information on genomic sequences from human coronaviruses. (B) An evolutionary tree constructed from representative genomic sequences. (C) A functional annotation of viral mutati
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Annotated screenshots of genome tables. (A) Sortable and filterable table. ... Open Access
Published: 26 November 2025
Figure 3.
Annotated screenshots of genome tables. (A) Sortable and filterable table. (B) Genome context menu: provides access to additional features. (C) ‘Show columns and filters’ bar: clicking on this bar expands settings to add more metadata columns to the table and apply filters.
Journal Article
Automated annotation and validation of human respiratory virus sequences using VADR Open Access
Database, Volume 2025, 2025, baaf078, https://doi.org/10.1093/database/baaf078
Published: 26 November 2025
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VADR model development of human respiratory viruses. (A) Annual increase in... Open Access
Published: 26 November 2025
Figure 1.
VADR model development of human respiratory viruses. (A) Annual increase in complete genome submissions to NCBI GenBank for human respiratory viruses. The upper plot shows submissions for seasonal respiratory viruses: human metapneumovirus (hMPV), human coronaviruses (HCoV-229E, -HKU1, -NL63, and -O
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Screenshot illustrating an example of target exploration in the HCoVDB data... Open Access
Published: 26 November 2025
Figure 4.
Screenshot illustrating an example of target exploration in the HCoVDB database. (A) Basic information on the SARS-CoV-2 protein NSP1. (B) Options to view detailed molecular docking results by selecting the drug ‘Montelukast’.
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Screenshots of genomic structure and annotation visualizations in MoPSeq-DB... Open Access
Published: 26 November 2025
Figure 4.
Screenshots of genomic structure and annotation visualizations in MoPSeq-DB. These annotated screenshots illustrate the interactive genomic structure graphs available in MoPSeq-DB, providing users with various interactive options for in-depth exploration of genomic data. (A) For viruses: 1—horizonta
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Phylogenetic tree visualization. This annotated screenshot displays the int... Open Access
Published: 26 November 2025
Figure 5.
Phylogenetic tree visualization. This annotated screenshot displays the interactive phylogenetic tree available on MoPSeq-DB for Vibrio aestuarianus , providing users with several interactive options. 1—Export: save the tree in Newick format or as an image with the current selection; 2—information:
Journal Article
CircAI: a comprehensive database of CircRNA associated with A-to-I RNA editing Open Access
Database, Volume 2025, 2025, baaf075, https://doi.org/10.1093/database/baaf075
Published: 22 November 2025
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An overview of the ecosystem is provided. Panel (a) shows the extract-trans... Open Access
Published: 22 November 2025
Figure 4.
An overview of the ecosystem is provided. Panel (a) shows the extract-transform-load (ETL) process. Panel (b) Shows examples of tools provided (top) and tools that could easily be used. Panel (c) Notes how these user communities can create reproducible outputs.
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Global characteristics of RNA editing. (A) Number of samples for each speci... Open Access
Published: 22 November 2025
Figure 2.
Global characteristics of RNA editing. (A) Number of samples for each species. (B) Number of editing sites identified in each species. (C) Number of 12 editing types per species. (D) Distribution of RNA editing sites in different genomic regions. (E) Functional annotations of RNA editing sites for e
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Characterization of different species of circRNAs. (A) Number of circRNAs i... Open Access
Published: 22 November 2025
Figure 3.
Characterization of different species of circRNAs. (A) Number of circRNAs in different species. (B) Full-length sequences of circRNAs for each species. (C) The junction ratio of circRNAs for each species. (D) Percentage of circRNA types.
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Comprehensive view of CircAI database. Open Access
Published: 22 November 2025
Figure 5.
Comprehensive view of CircAI database.
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The page of CircAI’s (A) circRNA and (B) RNA editing detailed information. Open Access
Published: 22 November 2025
Figure 6.
The page of CircAI’s (A) circRNA and (B) RNA editing detailed information.
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An example of the documentation for a single variable. The values associate... Open Access
Published: 22 November 2025
Figure 1.
An example of the documentation for a single variable. The values associated with ‘Variable Name’, ‘SAS Label’, and ‘Target’ are extracted and used as metadata. The Table describes the code used in the raw SAS data file; the ‘Value Description’ column gives the English description of what the code m
