James W. Brown

Associate Professor & Undergraduate Coordinator
Department of Microbiology, NC State University

BioEdit: A User-friendly Biological Sequence Alignment Editor and Analysis Program for Windows 95/98/NT

Thomas A. Hall
Department of Microbiology
North Carolina State University

Abstract Submission for a poster – Local ASM 1999


BioEdit is a user-friendly sequence alignment editor and analysis package that is offered free of charge for Windows 95/98/NT systems.  BioEdit is a full-featured nucleic acid/protein alignment editor that offers several modes of easy hand-alignment, split-window views, user-defined colors, information-based shading, auto-integration with ClustalW (1), local/internet BLAST (2) and other links to the WWW, restriction-mapping, annotatable plasmid-drawing, box-shading with full color-capability, several built-in analysis options, and a graphical interface for configuring further interfaces to automatically run external analysis programs.  BioEdit is also customizable to user preferences with user-defined menu shortcuts and correct handling of all fonts.  Among the built-in analyses offered are a set of RNA comparative analysis tools including covariation (3, 4), potential-pairings (3, 4) and mutual information (5) analysis.  BioEdit offers the tools required to create and manipulate an alignment, run comparative analyses from the edit window, and view and analyze the data through interactive 2-D graphical matrix plots, area plots, and a rich-text editor.  This presentation describes a rough sample analysis of the secondary structure of bacterial RNase P RNA (excluding the high G+C Gram-Positive group) by mutual information probing.  An initial scanning of mutual information data via the graphical analysis tools reveals all major helices that exist in the E. coli structure (6, 7).  An incomplete overview of some of BioEdit’s other features is also presented.


1.  Thompson, J.D., Higgins, D.G and Gibson, T.J. (1994) Nucleic Acids Res., 22: 4673-4680.
2.  Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J.  (1990)  J. Mol. Biol. 215: 403-410.
3.  Gutell R.R., Weiser, B., Woese, C.R., Noller, H.F.  (1985)   Prog. Nucleic Acid Res. Mol. Biol32: 155-216.
4.  Brown, J.W.  (1991)  Comput. Appl. Biosci. 7: 391-393.
5.  Gutell, R.R., Power, A., Hertz, G.Z., Putz, E.J. and Stormo, G.D.  (1992)  Nucleic Acids Res20: 5785-5795.
6.  Pace, N.R. and Brown, J.W.  (1995)  J. Bacteriol177: 1919-1928.  
7.  Brown, J.W., Nolan, J.M., Haas, E.S., Rubio, M.A.T., Major, F. and Pace, N.R.  (1996)  Proc. Natl. Acad. Sci. USA  93: 3001-3006.

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