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PMID: 9358182 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

RnaViz, a program for the visualisation of RNA secondary structure.

Nucleic acids research ·Vol. 25 ·No. 22 ·1997-11-15 ·Pages 4679-84

De Rijk P, De Wachter R

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.

MeSH Terms

Base Sequence Computer Simulation Image Processing, Computer-Assisted Models, Molecular Molecular Sequence Data Nucleic Acid Conformation RNA/chemistry Software User-Computer Interface

Chemicals

RNA

Authors & Affiliations

2 authors, click to expand affiliations / ORCID

De Rijk P

Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium.

De Wachter R

References (14)

14 references, click to expand

Generating non-overlapping displays of nucleic acid secondary structure.
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):75-88 PMID: 6694904
An RNA secondary structure workbench.
Nucleic Acids Res. 1988 Mar 11;16(5):1789-98 PMID: 2451219
A secondary and tertiary structure editor for nucleic acids.
Comput Appl Biosci. 1988 Mar;4(1):143-6 PMID: 3382988
Graphics of RNA secondary structure; towards an object-oriented algorithm.
Comput Appl Biosci. 1987 Jun;3(2):99-103 PMID: 2455587
Conserved sequences and structures of group I introns: building an active site for RNA catalysis--a review.
Gene. 1988 Dec 20;73(2):259-71 PMID: 3072259
The functional role of ribosomal RNA in protein synthesis.
Cell. 1989 May 19;57(4):525-9 PMID: 2655923
A quantitative map of nucleotide substitution rates in bacterial rRNA.
Nucleic Acids Res. 1996 Sep 1;24(17):3381-91 PMID: 8811093
Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA--a review.
Gene. 1989 Oct 15;82(1):65-75 PMID: 2479592
Computer modeling and display of RNA secondary and tertiary structures.
Methods Enzymol. 1990;183:318-30 PMID: 1690337
Structural analysis by energy dot plot of a large mRNA.
J Mol Biol. 1993 Sep 20;233(2):261-9 PMID: 8377202
Automatic display of RNA secondary structures.
Comput Appl Biosci. 1993 Oct;9(5):551-61 PMID: 7507400
DCSE, an interactive tool for sequence alignment and secondary structure research.
Comput Appl Biosci. 1993 Dec;9(6):735-40 PMID: 7511479
CARD: a drawing tool for RNA secondary structure models.
Biotechniques. 1995 Jun;18(6):1060-3 PMID: 7546709
Comparative and functional anatomy of group II catalytic introns--a review.
Gene. 1989 Oct 15;82(1):5-30 PMID: 2684776

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/25.22.4679

Published

1997-11-15

Pages

4679-84

Language

English

Region

England

NLM ID

0411011

PMCID

PMC147081

Subset

External Links

PubMed source DOI: 10.1093/nar/25.22.4679 PMC Full Text View journal details

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