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NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures

Bansal, Manju and Bhattacharyya, D and Ravi, B (1995) NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures. In: CABIOS / Computer Applications in the Biosciences, 11 (3). pp. 281-287.

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Official URL: http://www.ncbi.nlm.nih.gov/pubmed/7583696

Abstract

Software packages NUPARM and NUCGEN, are described, which can be used to understand sequence directed structural variations in nucleic acids, by analysis and generation of non-uniform structures. A set of local inter basepair parameters (viz. tilt, roll, twist, shift, slide and rise) have been defined, which use geometry and coordinates of two successive basepairs only and can be used to generate polymeric structures with varying geometries for each of the 16 possible dinucleotide steps. Intra basepair parameters, propeller, buckle, opening and the C6...C8 distance can also be varied, if required, while the sugar phosphate backbone atoms are fixed in some standard conformation ill each of the nucleotides. NUPARM can be used to analyse both DNA and RNA structures, with single as well as double stranded helices. The NUCGEN software generates double helical models with the backbone fixed in B-form DNA, but with appropriate modifications in the input data, it can also generate A-form DNA ar rd RNA duplex structures.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Oxford University Press.
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 12 Jan 2010 05:53
Last Modified: 12 Jan 2010 05:53
URI: http://eprints.iisc.ernet.in/id/eprint/25223

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