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

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dc.contributor.authorTu, Shin-Lin
dc.contributor.authorStaheli, Jeannette P.
dc.contributor.authorMcClay, Colum
dc.contributor.authorMcLeod, Kathleen
dc.contributor.authorRose, Timothy M.
dc.contributor.authorUpton, Chris
dc.date.accessioned2019-01-24T20:10:54Z
dc.date.available2019-01-24T20:10:54Z
dc.date.copyright2018en_US
dc.date.issued2018
dc.description.abstractBase-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.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.description.sponsorshipThis research was funded by a Discovery Grant from the Natural Sciences and Engineering Research Council of Canada (RGPIN-2015-04953).en_US
dc.identifier.citationTu, S., Staheli, J.P., McClay, C., McLeod, K., Rose, T.M. & Upton, C. (2018). Base- By-Base Version 3: New Comparative Tools for Large Virus Genomes. Viruses, 10(11), 637. https://doi.org/10.3390/v10110637en_US
dc.identifier.urihttps://doi.org/10.3390/v10110637
dc.identifier.urihttp://hdl.handle.net/1828/10540
dc.language.isoenen_US
dc.publisherVirusesen_US
dc.subjectbioinformatics
dc.subjectvirus
dc.subjectcomparative genomics
dc.subjectsoftware
dc.subjectBase-By-Base
dc.subjectBBB
dc.subjectpoxvirus
dc.subjectASFV
dc.subjectMSA
dc.subject.departmentDepartment of Biochemistry and Microbiology
dc.titleBase-By-Base Version 3: New Comparative Tools for Large Virus Genomesen_US
dc.typeArticleen_US

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