THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. It is a database and web application describing the genome organization and providing analytical tools for the 938 known species of RNA virus. It can identify submitted nucleotide sequences, can place them into multiple whole-genome alignments (in species where more than one isolate has been fully sequenced) and contains translated genome sequences for all species. It has been created for two main purposes: to facilitate the comparative analysis of RNA viruses and to become a hub for other, more specialised virus Web sites.

Endpoint Protection: Protects endpoint devices from malware attacks.Network Protection: Protects networks from malware infiltration and spread.Database Protection: Protects databases from malware attacks.Web Protection: Protects web browsers and applications from malware attacks.Email Protection: Protects email systems from malware attacks. Recent developments include: September 2023: Zscaler, Inc. revealed a partnership with CrpowdStrike and Imprivata to offer medical institutions a zero-trust cybersecurity solution for the device to the cloud. Zscaler's recent integration with the Imprivata Digital Identity Platform offers visibility, threat prevention, and traceability for end-to-end, multi-user, shared device access management, helping organizations comply with regulatory requirements., June 2023: Libyan Spider, a platform that specializes in cloud hosting, and Monarx partnered to introduce cutting-edge malware prevention into the Libyan Spider ecosystem. Through this partnership, Monarx provides the platform with highly scalable signatureless scanning technology.. Key drivers for this market are: Stricter data privacy laws (e.g., GDPR, CCPA) are pushing organizations to implement comprehensive malware protection to ensure compliance and avoid penalties for data breaches. Potential restraints include: Some malware protection solutions can impact system performance, slowing down devices or networks, which may discourage organizations from adopting or fully utilizing these tools. Notable trends are: AI and machine learning are being increasingly integrated into malware protection solutions to enhance threat detection, identify new attack patterns, and provide more proactive defenses against emerging malware.

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The euHCVdb is a Hepatitis C Virus database oriented towards protein sequence, structure and function analyses and structural biology of HCV. In order to make the existing HCV databases as complementary as possible, the current developments are coordinated with the other databases (Japan and Los Alamos) as part of an international collaborative effort. It is monthly updated from the EMBL Nucleotide sequence database and maintained in a relational database management system. Programs for parsing the EMBL database flat files, annotating HCV entries, filling up and querying the database used SQL and Java programming languages. Great efforts have been made to develop a fully automatic annotation procedure thanks to a reference set of HCV complete annotated well-characterized genomes of various genotypes. This automatic procedure ensures standardization of nomenclature for all entries and provides genomic regions/proteins present in the entry, bibliographic reference, genotype, interesting sites or domains, source of the sequence and structural data that are available as protein 3D models. Hepatitis C, Hepatitis C Virus, Hepatitis C Virus protein .

This is a custom-built blast database of higher plant viruses and viroids.

A challenge associated with the bioinformatics analysis of sequencing data for diagnostic purposes is the dependency on sequence databases for taxonomic assignment of detection. Although public databases such as the GenBank database maintained at NCBI are the most up to date, the enormous nature of these databases limits their portability across different computing resources. Moreover, sequencing data submitted by users to these public databases may not be accurate, and annotations provided in the GenBank record, such as the taxonomy assignment, which is crucial for accurate diagnosis, may be inaccurate and/or out of data. Additionally, the descriptors of the sequences in the public databases are not harmonized and lack taxonomic information posing an additional challenge to validate sequence homology-based pathogen detections.

The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms.

IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. For the convenience of efficient data utilization, our Q-Filter system classifies and ranks all nucleotide sequences into 7 categories according to sequence content and integrity. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. A searching system is developed for users to retrieve a combination of different data types by setting various search options. To facilitate analysis of the global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) is developed to display worldwide geographic distribution of the viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment tools and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to the pre-computed alignments and polymorphism analysis of influenza virus genes and proteins and presents the results by SNP distribution plots and minor allele distributions. IVDB aims to be a powerful information resource and an analysis workbench for scientists working on IV genetics, evolution, diagnostics, vaccine development, and drug design.

NCBI Virus is an integrative, value-added resource designed to support retrieval, display and analysis of a curated collection of virus sequences and large sequence datasets. Its goal is to increase the usability of viral sequence data archived in GenBank and other NCBI repositories. This resource includes resources previously included in HIV-1, Human Protein Interaction Database, Influenza Virus Resource, and Virus Variation.

description: This facility acts as a fusion point for bridging ARL's research in tactical and operational Information Assurance (IA) areas and the development and assessment of improvements to IA processes including new monitoring tools, test beds, assessment methodologies, and malware/forensic analysis. The facility is equipped with a state-of-the-art intrusion detection system (IDS) framework, incident databases, and other tools to support operations that continually monitor and augment missions around the world.; abstract: This facility acts as a fusion point for bridging ARL's research in tactical and operational Information Assurance (IA) areas and the development and assessment of improvements to IA processes including new monitoring tools, test beds, assessment methodologies, and malware/forensic analysis. The facility is equipped with a state-of-the-art intrusion detection system (IDS) framework, incident databases, and other tools to support operations that continually monitor and augment missions around the world.

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. A collection of cDNA, gene and protein records of cytokines deposited in public databases provides various information about the cytokine members of vertebrates in other databases including NCBI GenBank, Swiss-Prot, UniGene, TIGR (The Institute for Genomic Research) Gene Indices, Ensembl, Entrez Gene, Mouse Genome Informatics (MGI) and Rat Genome Database (RGD). It also provides orthologous relationship of cytokine members and includes novel members identified in the databases.

Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH.

Viruses are increasingly viewed as vital components of the human gut microbiota, while their roles in health and diseases remain incompletely understood. Here, we first sequenced and analyzed the 37 metagenomic and 18 host metabolomic samples related to irritable bowel syndrome (IBS) and found that some shifted viruses between IBS and controls covaried with shifted bacteria and metabolites. Especially, phages that infect beneficial lactic acid bacteria depleted in IBS covaried with their hosts. We also retrieved public whole-genome metagenomic datasets of another four diseases (type 2 diabetes, Crohn’s disease, colorectal cancer, and liver cirrhosis), totaling 438 samples including IBS, and performed uniform analysis of the gut viruses in diseases. By constructing disease-specific co-occurrence networks, we found viruses actively interacting with bacteria, negatively correlated with possible dysbiosis-related and inflammation-mediating bacteria, increasing the connectivity between bacteria modules, and contributing to the robustness of the networks. Functional enrichment analysis showed that phages interact with bacteria through predation or expressing genes involved in the transporter and secretion system, metabolic enzymes, etc. We further built a viral database to facilitate systematic functional classification and explored the functions of viral genes on interacting with bacteria. Our analyses provided a systematic view of the gut virome in the disease-related microbial community and suggested possible positive roles of viruses concerning gut health.

The South American continent presents a great diversity of biomes, whose ecosystems are constantly threatened by the expansion of human activity. The emergence and re-emergence of viral populations with impact on the human population and ecosystem have shown increases in the last decades. In deference to the growing accumulation of genomic data, we explore the potential of South American-related public databases to detect signals that contribute to virosphere research. Therefore, our study aims to investigate public databases with emphasis on the surveillance of viruses with medical and ecological relevance. Herein, we profiled 120 “sequence read archives” metagenomes from 19 independent projects from the last decade. In a coarse view, our analyses identified only 0.38% of the total number of sequences from viruses, showing a higher proportion of RNA viruses. The metagenomes with the most important viral sequences in the analyzed environmental models were 1) aquatic samples from the Amazon River, 2) sewage from Brasilia, and 3) soil from the state of São Paulo, while the models of animal transmission were detected in mosquitoes from Rio Janeiro and Bats from Amazonia. Also, the classification of viral signals into operational taxonomic units (OTUs) (family) allowed us to infer from metadata a probable host range in the virome detected in each sample analyzed. Further, several motifs and viral sequences are related to specific viruses with emergence potential from Togaviridae, Arenaviridae, and Flaviviridae families. In this context, the exploration of public databases allowed us to evaluate the scope and informative capacity of sequences from third-party public databases and to detect signals related to viruses of clinical or environmental importance, which allowed us to infer traits associated with probable transmission routes or signals of ecological disequilibrium. The evaluation of our results showed that in most cases the size and type of the reference database, the percentage of guanine–cytosine (GC), and the length of the query sequences greatly influence the taxonomic classification of the sequences. In sum, our findings describe how the exploration of public genomic data can be exploited as an approach for epidemiological surveillance and the understanding of the virosphere.

The most common backup was for databases in Poland in 2021. Three quarters of respondents performed servers and individual files backups. More than half made computer backups.

VIRUSBreakend database generated from NCBI 01 Apr 2021

Database of SARS-CoV-2 and other viruses. Integrates structural and dynamic insights with viral evolution for proteins coded by virus. Each virus within database has workflow performed on each protein. Workflow consists of protein modeling, molecular dynamic simulations, evolutionary analysis, and mapping of protein-protein interactions. On page for each protein is link to individual protein data folder system, video of protein rotating with conservation, details of protein function, widget to purchase 3D print of protein at cost of production, amino acid movement from molecular dynamic simulations, and table of data for each amino acid of protein.

We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologous public repository, RVDB-prot aims to provide reliable and accurately annotated unique entries, while including also an Hidden Markov Model (HMM) protein profiles database for distant protein searching.

Here are the data set and source code related to the paper: "A Framework for Developing Strategic Cyber Threat Intelligence from Advanced Persistent Threat Analysis Reports Using Graph-Based Algorithms"1- aptnotes-downloader.zip : contains source code that downloads all APT reports listed in https://github.com/aptnotes/data and https://github.com/CyberMonitor/APT_CyberCriminal_Campagin_Collections2- apt-groups.zip : contains all APT group names gathered from https://docs.google.com/spreadsheets/d/1H9_xaxQHpWaa4O_Son4Gx0YOIzlcBWMsdvePFX68EKU/edit?gid=1864660085#gid=1864660085 and https://malpedia.caad.fkie.fraunhofer.de/actorsand https://malpedia.caad.fkie.fraunhofer.de/actors3- apt-reports.zip : contains all deduplicated APT reports gathered from https://github.com/aptnotes/data and https://github.com/CyberMonitor/APT_CyberCriminal_Campagin_Collections4- countries.zip : contains country name list. 5- ttps.zip : contains all MITRE techniques gathered from https://attack.mitre.org/resources/attack-data-and-tools/6- malware-families.zip : contains all malware family names gathered from https://malpedia.caad.fkie.fraunhofer.de/families7- ioc-searcher-app.zip : contains source code that extracts IoCs from APT reports. Extracted IoC files are provided in report-analyser.zip. Original code repo can be found at https://github.com/malicialab/iocsearcher8- extracted-iocs.zip : contains extracted IoCs by ioc-searcher-app.zip9- report-analyser.zip : contains source code that searchs APT reports, malware families, countries and TTPs. I case of a match, it updates files in extracted-iocs.zip. 10- cti-transformation-app.zip : contains source code that transforms files in extracted-iocs.zip to CTI triples and saves into Neo4j graph database.11- graph-db-backup.zip : contains volume folder of Neo4j Docker container. When it is mounted to a Docker container, all CTI database becomes reachable from Neo4j web interface. Here is how to run a Neo4j Docker container that mounts folder in the zip:docker run -d --publish=7474:7474 --publish=7687:7687 --volume={PATH_TO_VOLUME}/DEVIL_NEO4J_VOLUME/neo4j/data:/data --volume={PATH_TO_VOLUME}/DEVIL_NEO4J_VOLUME/neo4j/plugins:/plugins --volume={PATH_TO_VOLUME}/DEVIL_NEO4J_VOLUME/neo4j/logs:/logs --volume={PATH_TO_VOLUME}/DEVIL_NEO4J_VOLUME/neo4j/conf:/conf --env 'NEO4J_PLUGINS=["apoc","graph-data-science"]' --env NEO4J_apoc_export_file_enabled=true --env NEO4J_apoc_import_file_enabled=true --env NEO4J_apoc_import_file_use_neo4j_config=true --env=NEO4J_AUTH=none neo4j:5.13.0web interface: http://localhost:7474username: neo4jpassword: neo4j

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

Public knowledge base specialized in the management and analysis of integrated virus-virus, virus-host and host-host interaction networks coupled to their functional annotations. It contains high quality and up-to-date information gathered and curated from public databases (VirusMint, Intact, HIV-1 database). It allows users to search by host gene, host/viral protein, gene ontology function, KEGG pathway, Interpro domain, and publication information. It also allows users to browse viral taxonomy.

hmmscan_DBs.tgz = tarball of compiled HMM databases (h3m files) (updated for hmm DB v3.1.1)

refseq_virus_prot.fasta.gz = tax database refseq: refseq virus protein seqs for mmseqs2 tax database

refseq_virus_prot_taxids.mmseqs_fmt.tsv = tax database refseq: tax info required for mmseqs2 refseq tax database annotation

ct3_hallmark_nr_cd90_refseq.faa.gz = tax database hallmark: hallmark proteins (per Cenote-Taker 3 search) from --- Genbank clustered NR virus (filtered for seqs with taxonomic labels at genus, family, and class level) (clustered at 90% AAI with cd-hit) AND refseq virus hallmark proteins (per Cenote-Taker 3 search)

ct3_hallmark_nr_cd90_refseq.prot_taxids.mmseqs_fmt.tsv = tax database hallmark: tax info required for mmseqs2 hallmark tax database annotation

cddid_all.tbl = CDD functional annotation table

viral_cdds_and_pfams_191028.txt = list of domain accessions commonly found in virus genomes