Journal
VIRUSES-BASEL
Volume 10, Issue 11, Pages -Publisher
MDPI
DOI: 10.3390/v10110637
Keywords
bioinformatics; virus; comparative genomics; software; Base-By-Base; BBB; poxvirus; ASFV; MSA
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Funding
- Natural Sciences and Engineering Research Council of Canada [RGPIN-2015-04953]
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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.
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