Proceedings of 11thNational Science Symposium on Recent Trends in Science and Technology (February 03, 2019) Organized by Christ College, Rajkot & Sponsored by Gujarat State Biotechnology Mission (GSBTM), DST, Govt. of Gujarat. Bioinformatics VIROINFORMATICS: DATABASES AND TOOLS Angelin George, John J. Georrge* Department of Bioinformatics, Christ College, Rajkot-360 005, Gujarat [email protected] ABSTRACT The amalgamation of virology and Bioinformatics has led to the development of a new field known as viroinformatics. More than 100 web servers and databases are currently available, which provides information regarding different viruses, for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc. The databases provide the tools for homology modelling, phylogenetic tree, multiple sequence alignment, 3D visualization. The need for computer-assisted technologies of genome structure, function and evolution of viruses is increasing immensely to tackle various challenges in virology. This review presents an overview of all the viroinformatics databases and tools developed to contribute to the development of the new potential drug. 1. INTRODUCTION Viruses are ubiquitous infectious agent known to have infected all types of life forms, from animals and plants to microorganisms such as bacteria and archaea. Viruses cause various human diseases; this includes common cold, influenza, chickenpox, and cold sores and serious diseases such as Ebola virus disease, dengue fever, AIDS, avian influenza, and severe acute respiratory syndrome (SARS). The possible connection between human herpesvirus 6 (HHV6) and neurological diseases such as multiple sclerosis and chronic fatigue syndrome is under investigation (Komaroff, 2006). Approximately 6 million deaths occur every year due to viruses, despite the availability of effective vaccines and treatments for several diseases. Thus, it is crucial to develop remedies against these viral invaders. A large amount of genomic and experimental data is generated due to advancement in molecular biology and Bioinformatics. To store, examine, and disseminate all this information, 144 viroinformatics resources have been developed. The International Committee on Taxonomy of Viruses (ICTV) performs naming and classifying virus lists 4,958 species. The genome of 8110 viral strains has been sequenced (NCBI Viral Genome Resource). Bioinformatics research works, including data analysis, development of tools and databases on the microorganisms, are growing gradually (Abouelwafa et al., 2017; George et al., 2018; George et al., 2017; Georrge et al., 2011; Georrge et al., 2012; Georrge, 2016; Kotadiya et al., 2015; Lijo et al., 2012; Nishita et al., 2015; Nishita et al., 2016; Ranipa et al., 2018; Sakina et al., 2016; Sharma et al., 2014; Trivedi et al., 2016a, 2016b; Ukani et al., 2011; Vaidya et al., 2018). The powerful viroinformatics resources have been developed that provides unprecedented opportunities to address fundamental questions in virology. Bioinformatic analysis of viruses includes analyzing any novel sequences, such as gene identification, gene functional annotation, and analysis of phylogenetic relationships. As the viral genome is of small size, it is possible to sequence large numbers of isolates, which calls for specific methods of analysis. However, the current sequencing technologies available for viral genomes pose challenges because most analysis steps are not easily automated (Tumpey et al., 2005). 2. VIRUS-CENTERED RESOURCES The biodiversity of viruses and its coverage of multiple scales is challenging for algorithm and software development (Hufsky et al., 2018). Recently, many new databases and tools are available to virologists that will be discussed in the following section. Baculoviruses and Papillomaviruses Baculoviruses are a family of viruses that infect insects. They have a large double-stranded DNA (dsDNA) genome that can accommodate multiple additional foreign genes (Kamita et al., 2010). The www.virology.ca is a database that provides easy access to the genes, gene families, and genomes of the different virus families, including Baculoviruses. Human Papillomavirus (HPV) is an infection caused by papillomavirus that can spread through skin-to-skin contact (Table 1). A Papillomavirus www.christcollegerajkot.edu.in, © Christ College, Rajkot, India ISBN: 9788192952147, Page No. 117 Proceedings of 11thNational Science Symposium on Recent Trends in Science and Technology (February 03, 2019) Organized by Christ College, Rajkot & Sponsored by Gujarat State Biotechnology Mission (GSBTM), DST, Govt. of Gujarat. Bioinformatics Episteme (PaVE) database contains curated papillomavirus genomic sequences and provides several web-based sequence analysis tools (Van Doorslaer et al., 2016). Table 1: Resources of Baculoviruses and Papillomaviruses Resources Specific Features URL Baculoviruses virology.ca Database that provides access to https://4virology.net/ viral genomic information Papillomaviruses PaVE Access to papillomavirus http://pave.niaid.nih.gov sequences and analysis tools Dengue Virus and West Nile Virus Dengue virus is the causative agent of common arthropod-borne viral disease in man with 50–100 million infections per year. Till now, vaccines have been developed that can affect all the serotypes of the dengue virus. A set of the virus-specific database is available at NCBI, referred to as Virus Variation Resources (VVR) (Table 2). It is an integrated resource for the dengue virus and West Nile Virus, where the users can build complex queries and then apply various analysis tools to the result (Resch et al., 2009). The DengueNet is the World Health Organization’s central data management system for the global epidemiological surveillance of dengue fever (DF) and dengue haemorrhagic fever (DHF) (Lawrence, 2002). Table 2: Resources of Dengue Virus and West Nile Virus Resources Specific Features URL Dengue Virus and West Nile Virus NCBI-VVR Set of virus-specific database http://www.ncbi.nlm.nih.gov/genomes/Virus Variation/ Dengue Virus DengueNet Data management system for surveillance of dengue fever - Influenza Virus The human influenza virus is distributed worldwide. Influenza was brought to the forefront of the world’s attention due to the recent emergence of highly pathogenic avian influenza virus (AIV; H5N1) that resulted in the death of more than 100 people and the slaughter of millions of poultry in Asia, Europe and Africa (World Health Organization, http://www.who.int). Till now, ten web portals and tools have been developed solely for the influenza virus (Table 3). Influenza Virus Database (IVDB) was the first information resource to be developed containing both Beijing Institute of Genomics (BIG) data and published IV sequences after expert curation to ensure a high standard of accuracy completeness. Till now IVDB contains 43,875 influenza virus nucleotide sequences, 53,983 CDS sequences and 53,983 protein sequences. Two main features of IVDB are (i) Sequence Distribution Tool: It facilitates IV global transmission and evolution analysis. (ii) IV Sequence Quality Filter System: The nucleotide sequences are classified and ranked in 7 categories according to sequence content and integrity by the Q-filter system (Chang et al., 2006). www.christcollegerajkot.edu.in, © Christ College, Rajkot, India ISBN: 9788192952147, Page No. 118 Proceedings of 11thNational Science Symposium on Recent Trends in Science and Technology (February 03, 2019) Organized by Christ College, Rajkot & Sponsored by Gujarat State Biotechnology Mission (GSBTM), DST, Govt. of Gujarat. Bioinformatics Table 3: Resources of Influenza Virus Resources Specific features URL NCBI-IVR Integrated information resource and analysis http://influenza.psych.ac.cn/ platform for genetic, genomic, and phylogenetic studies of influenza virus. FluTE Influenza epidemic simulation tool https://www.cs.unm.edu/~dlch ao/flute/ IRD Provides various visualization and analysis tools https://www.fludb.org/brc/hom for comparative genomics e.spg?decorator =influenza FluGenome Web portal for genotyping influenza A virus https://omictools.com/flugeno me-tool IVDB An integrated information resource and analysis http://influenza.big.ac.cn/ platform for influenza virus research EpiFlu Provides access to influenza virus sequences, http://platform.gisaid.org related clinical and epidemiological data associated with human viruses GiRaF Identifies influenza virus reassortments http://kingsfordlab.cbd.cmu.ed u/ OpenFluDB Contains genomic and protein sequences as well http://openflu.vital- as epidemiological data from more than 25’000 it.ch/browse.php isolates. ISED Establishes influenza genomic sequences and http://influenza.cdc.go.kr compares the user’s sequences with those of vaccine strains. ATIVS Analysis tools for influenza virus surveillance. http://influenza.nhri.org.tw/AT IVS/ NCBI-IVR is the most cited resources and provides tools for genome annotation of influenza virus such as FLAN (FLu ANnotation) for user-provided influenza A virus or influenza B virus sequences (Bao et al., 2007). IRD is a public-accessible resource that integrates genomic, proteomic, immune epitope, and surveillance data from various sources, including public databases, computational algorithms and scientific literature (Squires et al., 2012). Apart from this, FluGenome is a developed tool for genotyping influenza A virus and identifies reassortment