Base-By-Base version 2 : single nucleotide-level analysis of whole viral genome alignments

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dc.contributor.authorHillary, William
dc.contributor.authorLin, Song-Han
dc.contributor.authorUpton, Christopher
dc.date.accessioned2013-10-29T21:12:44Z
dc.date.available2013-10-29T21:12:44Z
dc.date.copyright2011en_US
dc.date.issued2011-06-14
dc.descriptionBioMed Centralen_US
dc.description.abstractBackground: Base-By-Base is a Java-based multiple sequence alignment editor. It is capable of working with protein and DNA molecules, but many of its unique features relate to the manipulation of the genomes of large DNA viruses such as poxviruses, herpesviruses, baculoviruses and asfarviruses (1-400 kb). The tool was built to serve as a platform for comparative genomics at the level of individual nucleotides. Results: In version 2, BBB-v2, of Base-By-Base we have added a series of new features aimed at providing the bench virologist with a better platform to view, annotate and analyze these complex genomes. Although a poxvirus genome, for example, may be less than 200 kb, it probably encodes close to 200 proteins using multiple classes of promoters with frequent overlapping of promoters and coding sequences and even some overlapping of genes. The new features allow users to 1) add primer annotations or other data sets in batch mode, 2) export differences between sequences to other genome browsers, 3) compare multiple genomes at a single nucleotide level of detail, 4) create new alignments from subsets/subsequences of a very large master alignment and 5) allow display of summaries of deep RNA sequencing data sets on a genome sequence. Conclusion: BBB-v2 significantly improves the ability of virologists to work with genome sequences and provides a platform with which they can use a multiple sequence alignment as the basis for their own editable documents. Also, a .bbb document, with a variety of annotations in addition to the basic coding regions, can be shared among collaborators or made available to an entire research community. The program is available via Virology.ca using Java Web Start and is platform independent; the Java 1.5 virtual machine is required.en_US
dc.description.reviewstatusRevieweden_US
dc.description.scholarlevelFacultyen_US
dc.identifier.citationHillary et al.: Base-By-Base version 2: single nucleotide-level analysis of whole viral genome alignments. Microbial Informatics and Experimentation 2011 1:2.en_US
dc.identifier.urihttp://www.microbialinformaticsj.com/content/1/1/2
dc.identifier.urihttp://dx.doi.org/10.1186/2042-5783-1-2
dc.identifier.urihttp://hdl.handle.net/1828/5015
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.subject.departmentDepartment of Biochemistry and Microbiology
dc.titleBase-By-Base version 2 : single nucleotide-level analysis of whole viral genome alignmentsen_US
dc.typeArticleen_US

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