In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation sequencing of DNA genomes and mRNA transcripts and mass spectrometry of proteins. Perhaps, however, it is genome sequencing that impacts a virologist the most. In 2017, more than 480 complete genome sequences of poxviruses have been generated, and are constantly used in many different ways by almost all molecular virologists. Matching this growth in data acquisition is an explosion of the relatively new field of bioinformatics, providing databases to store and organize this valuable/expensive data and algorithms to analyze it. For the bench virologist, access to intuitive, easy-to-use, software is often critical for performing bioinformatics-based experiments. Three common hurdles for the researcher are (1) selection, retrieval, and reformatting genomics data from large databases; (2) use of tools to compare/analyze the genomics data; and (3) display and interpretation of complex sets of results. This chapter is directed at the bench virologist and describes the software that helps overcome these obstacles, with a focus on the comparison and analysis of poxvirus genomes. Although poxvirus genomes are stored in public databases such as GenBank, this resource can be cumbersome and tedious to use if large amounts of data must to be collected. Therefore, we also highlight our Viral Orthologous Clusters database system and integrated tools that we developed specifically for the management and analysis of complete viral genomes.
Keywords: BBB; BLAST; Bioinformatics; Dotplot; Genomics; JDotter; MSA; Multiple sequence alignment; Poxvirus; Smallpox; VGO; VOCs; Vaccinia virus.