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Viruses. 2018 Nov 15;10(11). pii: E637. doi: 10.3390/v10110637.

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

Author information

1
Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada. cindytu@uvic.ca.
2
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98101, USA. jeannette.staheli@seattlechildrens.org.
3
Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada. colummcclay@hotmail.com.
4
Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada. kathleen_mcleod14@hotmail.com.
5
Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98101, USA. trose@u.washington.edu.
6
Department of Pediatrics, University of Washington, Seattle, WA 98195, USA. trose@u.washington.edu.
7
Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 2Y2, Canada. cupton@uvic.ca.

Abstract

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.

KEYWORDS:

ASFV; BBB; Base-By-Base; MSA; bioinformatics; comparative genomics; poxvirus; software; virus

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