Alvira: comparative genomics of viral strains

Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine

The world is changing due to factors like bioterrorism, massive environmental changes, globalization of trade and commerce, growing urbanization, changing climate, and pollution. Numerous diseases have emerged because of these factors, especially in companion and food-producing animals. Numerous pathogens have established themselves in naïve populations, harming reproduction, productivity, and health. Bioinformatics is considered a valuable tool in infectious disease research, as it provides a comprehensive overview of the identification of pathogens, their genetic makeup, and their evolutionary relationship. Therefore, there is an urgent need for a novel bioinformatics approach to help decipher and model viral epidemiology and informatics on domestic animals and livestock. With significant advancements in bioinformatics and NGS, researchers can now identify contigs, which are contiguous sequences of DNA that are assembled from overlapping fragments, assemble a complete genome, perform phylogenetic analysis to diagnose, investigate the risk of viral diseases in animals, handle and share large biological datasets across various species. Additionally, multi-omics data integration further deepens our understanding of homology, divergence, mutations, and evolutionary relationships, providing a comprehensive perspective on the molecular mechanisms driving animal pathogens infections. This review aims to reveal the importance of utilizing the multidisciplinary areas of bioinformatics, genomics, proteomics, transcriptomics, metabolomics, and metagenomics and their roles in studying viral infectious diseases in veterinary medicine that will eventually improve the health of animals.

Bioinformatics Applications in Advancing Animal Virus Research

Viruses serve as infectious agents for all living entities. There have been various research groups that focus on understanding the viruses in terms of their host-viral relationships, pathogenesis and immune evasion. However, with the current advances in the field of science, now the research field has widened up at the ‘omics’ level. Apparently, generation of viral sequence data has been increasing. There are numerous bioinformatics tools available that not only aid in analysing such sequence data but also aid in deducing useful information that can be exploited in developing preventive and therapeutic measures. This chapter elaborates on bioinformatics tools that are specifically designed for animal viruses as well as other generic tools that can be exploited to study animal viruses. The chapter further provides information on the tools that can be used to study viral epidemiology, phylogenetic analysis, structural modelling of proteins, epitope recognition and open reading frame (ORF) recognition and tools that enable to analyse host-viral interactions, gene prediction in the viral genome, etc. Various databases that organize information on animal and human viruses have also been described. The chapter will converse on overview of the current advances, online and downloadable tools and databases in the field of bioinformatics that will enable the researchers to study animal viruses at gene level.

viruSITE-integrated database for viral genomics

Viruses are the most abundant biological entities and the reservoir of most of the genetic diversity in the Earth's biosphere. Viral genomes are very diverse, generally short in length and compared to other organisms carry only few genes. viruSITE is a novel database which brings together high-value information compiled from various resources. viruSITE covers the whole universe of viruses and focuses on viral genomes, genes and proteins. The database contains information on virus taxonomy, host range, genome features, sequential relatedness as well as the properties and functions of viral genes and proteins. All entries in the database are linked to numerous information resources. The above-mentioned features make viruSITE a comprehensive knowledge hub in the field of viral genomics.

The web interface of the database was designed so as to offer an easy-to-navigate, intuitive and user-friendly environment. It provides sophisticated text searching and a taxonomy-based browsing system. viruSITE also allows for an alternative approach based on sequence search. A proprietary genome browser generates a graphical representation of viral genomes. In addition to retrieving and visualising data, users can perform comparative genomics analyses using a variety of tools.

Database URL: http://www.virusite.org/

Unraveling the web of viroinformatics: computational tools and databases in virus research

The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain--viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article.