Generating non-overlapping displays of nucleic acid secondary structure.

Nucleic acids research ·Vol. 12 ·No. 1 Pt 1 ·1984-01-11 ·Pages 75-88

Shapiro BA, Maizel J, Lipkin LE, Currey K, Whitney C

Abstract

A new algorithm is presented which permits the display of nucleic acid secondary structure by computer. This algorithm circumvents the problem of overlapping portions of the molecule which is inherent in some other drawing programs. The results from this algorithm may also be used as input to the drawing algorithm previously reported in this journal [1] to untangle most of a drawing. The algorithm also represents the molecule in a form which makes visual comparisons for similarity quite easy since it guarantees that comparable features will reside in the same relative position in the drawings when the drawings are normalized.

MeSH Terms

Base Sequence Computers Hydrogen Bonding Nucleic Acid Conformation Nucleic Acids RNA, Ribosomal

Chemicals

Nucleic Acids RNA, Ribosomal

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Shapiro B A

Maizel J

Lipkin L E

Currey K

Whitney C

References (8)

8 references, click to expand

The intervening sequence of a mouse beta-globin gene is transcribed within the 15S beta-globin mRNA precursor.
Proc Natl Acad Sci U S A. 1978 Mar;75(3):1309-13 PMID: 274720
Computer method for predicting the secondary structure of single-stranded RNA.
Nucleic Acids Res. 1978 Sep;5(9):3365-87 PMID: 100768
Fast algorithm for predicting the secondary structure of single-stranded RNA.
Proc Natl Acad Sci U S A. 1980 Nov;77(11):6309-13 PMID: 6161375
Method for predicting RNA secondary structure.
Proc Natl Acad Sci U S A. 1975 Jun;72(6):2017-21 PMID: 1056009
Computer-aided prediction of RNA secondary structures.
Nucleic Acids Res. 1982 Jan 11;10(1):403-19 PMID: 6174937
An interactive technique for the display of nucleic acid secondary structure.
Nucleic Acids Res. 1982 Nov 11;10(21):7041-52 PMID: 7177857
Splice junctions: association with variation in protein structure.
Science. 1983 Jun 10;220(4602):1125-9 PMID: 6344214
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
Nucleic Acids Res. 1981 Jan 10;9(1):133-48 PMID: 6163133

Article Info

Journal

Nucleic acids research

Abbr.

Nucleic Acids Res

ISSN

0305-1048

DOI

10.1093/nar/12.1part1.75

Published

1984-01-11

Pages

75-88

Language

English

Region

England

NLM ID

0411011

PMCID

PMC320985

Subset

External Links

PubMed source DOI: 10.1093/nar/12.1part1.75 PMC Full Text View journal details

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Generating non-overlapping displays of nucleic acid secondary structure.

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