Abstract
RnaViz is a user-friendly, portable, windows-type program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files. The layout of a structure can be changed easily. Display of special structural elements such as pseudo-knots or unformatted areas is possible. Sequences can be automatically numbered, and several other types of labels can be used to annotate particular bases or areas. Although the program does not try to produce an initially non-overlapping drawing, the layout of a properly positioned structure drawing can be applied to a newly created drawing using skeleton files. In this way a range of similar structures can be drawn with a minimum of effort. Skeletons for several types of RNA molecule are included with the program.
Full Text
The Full Text of this article is available as a PDF (259.2 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Cech T. R. Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review. Gene. 1988 Dec 20;73(2):259–271. doi: 10.1016/0378-1119(88)90492-1. [DOI] [PubMed] [Google Scholar]
- Cedergren R., Gautheret D., Lapalme G., Major F. A secondary and tertiary structure editor for nucleic acids. Comput Appl Biosci. 1988 Mar;4(1):143–146. doi: 10.1093/bioinformatics/4.1.143. [DOI] [PubMed] [Google Scholar]
- Dahlberg A. E. The functional role of ribosomal RNA in protein synthesis. Cell. 1989 May 19;57(4):525–529. doi: 10.1016/0092-8674(89)90122-0. [DOI] [PubMed] [Google Scholar]
- De Rijk P., De Wachter R. DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci. 1993 Dec;9(6):735–740. doi: 10.1093/bioinformatics/9.6.735. [DOI] [PubMed] [Google Scholar]
- Gautheret D., Major F., Cedergren R. Computer modeling and display of RNA secondary and tertiary structures. Methods Enzymol. 1990;183:318–330. doi: 10.1016/0076-6879(90)83021-z. [DOI] [PubMed] [Google Scholar]
- Jacobson A. B., Zuker M. Structural analysis by energy dot plot of a large mRNA. J Mol Biol. 1993 Sep 20;233(2):261–269. doi: 10.1006/jmbi.1993.1504. [DOI] [PubMed] [Google Scholar]
- Martinez H. M. An RNA secondary structure workbench. Nucleic Acids Res. 1988 Mar 11;16(5):1789–1798. doi: 10.1093/nar/16.5.1789. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns--a review. Gene. 1989 Oct 15;82(1):5–30. doi: 10.1016/0378-1119(89)90026-7. [DOI] [PubMed] [Google Scholar]
- Muller G., Gaspin C., Etienne A., Westhof E. Automatic display of RNA secondary structures. Comput Appl Biosci. 1993 Oct;9(5):551–561. doi: 10.1093/bioinformatics/9.5.551. [DOI] [PubMed] [Google Scholar]
- Pace N. R., Smith D. K., Olsen G. J., James B. D. Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review. Gene. 1989 Oct 15;82(1):65–75. doi: 10.1016/0378-1119(89)90031-0. [DOI] [PubMed] [Google Scholar]
- Shapiro B. A., Maizel J., Lipkin L. E., Currey K., Whitney C. Generating non-overlapping displays of nucleic acid secondary structure. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):75–88. doi: 10.1093/nar/12.1part1.75. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van de Peer Y., Chapelle S., De Wachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucleic Acids Res. 1996 Sep 1;24(17):3381–3391. doi: 10.1093/nar/24.17.3381. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Winnepenninckx B., Van de Peer Y., Backeljau T., De Wachter R. CARD: a drawing tool for RNA secondary structure models. Biotechniques. 1995 Jun;18(6):1060–1063. [PubMed] [Google Scholar]
- Yamamoto K., Sakurai N., Yoshikura H. Graphics of RNA secondary structure; towards an object-oriented algorithm. Comput Appl Biosci. 1987 Jun;3(2):99–103. doi: 10.1093/bioinformatics/3.2.99. [DOI] [PubMed] [Google Scholar]