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

Microbial Informatics and Experimentation
William HillaryChris Upton

Abstract

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. 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. BBB-v2 signif...Continue Reading

References

Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Nov 14, 2000·Virus Research·C UptonN L Harris
Apr 13, 2001·Bioinformatics·C Gille, C Frömmel
Jun 14, 2003·Journal of Virology·Chris UptonRachel L Roper
Jul 16, 2004·BMC Bioinformatics·Ryan BrodieChris Upton
Mar 1, 2006·Virus Research·E J LefkowitzC Upton
Sep 17, 2008·Current Protocols in Bioinformatics·Julie D ThompsonDes G Higgins
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Apr 23, 2010·BMC Biology·Oliver R Homann, Alexander D Johnson
Apr 30, 2010·Bioinformatics·Kazutaka Katoh, Hiroyuki Toh
May 26, 2010·Nucleic Acids Research·Amarendran R SubramanianBurkhard Morgenstern
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Zhilong YangBernard Moss

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Citations

Mar 15, 2014·PloS One·Chad SmithsonChris Upton
Nov 13, 2014·BMC Infectious Diseases·Mette T ChristiansenJudith Breuer
May 30, 2015·The Journal of General Virology·Clare FleischauerRachel L Roper
Nov 20, 2014·The Journal of General Virology·Raquel PortugalGünther M Keil
Jul 9, 2016·The Journal of General Virology·Mark A O'DeaChris Upton
Nov 9, 2016·Ticks and Tick-borne Diseases·Sara Tudela ZúqueteAlexandre Leitão
Feb 16, 2016·Scientific Reports·Justin H J NgMichelle L Baker
Sep 9, 2017·Viruses·Chad SmithsonChris Upton
May 6, 2014·Applied and Environmental Microbiology·Annika Gillis, Jacques Mahillon
Dec 28, 2016·Database : the Journal of Biological Databases and Curation·Matej StanoLubos Klucar
Sep 11, 2016·Virus Genes·Chad SmithsonChris Upton
Sep 19, 2018·Virus Genes·Jessica M JacobThomas B Waltzek
Jan 9, 2021·Microbiology Resource Announcements·Subir SarkerKarla J Helbig

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Software Mentioned

DIALIGN
- Base
MS Windows
JalView
Viral Genome Organizer
SimPlot
MUSCLE
SeaView
MAFFT
ClustalW

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