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Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes

Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada
Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, WA 98101, USA
Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
Author to whom correspondence should be addressed.
Viruses 2018, 10(11), 637;
Received: 25 October 2018 / Revised: 10 November 2018 / Accepted: 13 November 2018 / Published: 15 November 2018
(This article belongs to the Special Issue Virus Bioinformatics)
PDF [1324 KB, uploaded 15 November 2018]


Base-By-Base is a comprehensive tool for the creation and editing of multiple sequence alignments that is coded in Java and runs on multiple platforms. It can be used with gene and protein sequences as well as with large viral genomes, which themselves can contain gene annotations. This report describes new features added to Base-By-Base over the last 7 years. The two most significant additions are: (1) The recoding and inclusion of “consensus-degenerate hybrid oligonucleotide primers” (CODEHOP), a popular tool for the design of degenerate primers from a multiple sequence alignment of proteins; and (2) the ability to perform fuzzy searches within the columns of sequence data in multiple sequence alignments to determine the distribution of sequence variants among the sequences. The intuitive interface focuses on the presentation of results in easily understood visualizations and providing the ability to annotate the sequences in a multiple alignment with analytic and user data. View Full-Text
Keywords: bioinformatics; virus; comparative genomics; software; Base-By-Base; BBB; poxvirus; ASFV; MSA bioinformatics; virus; comparative genomics; software; Base-By-Base; BBB; poxvirus; ASFV; MSA

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Tu, S.-L.; Staheli, J.P.; McClay, C.; McLeod, K.; Rose, T.M.; Upton, C. Base-By-Base Version 3: New Comparative Tools for Large Virus Genomes. Viruses 2018, 10, 637.

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