RNA secondary structure 2D graphical representation without degeneracy

A two-dimensional graphical representation (2DGRR) of RNA secondary structures using a two Cartesian coordinates system has been derived for mathematical denotation of RNA structure. The 2DGRR resolves structure degeneracy and avoids loss of information and the limitation that different structures correspond to the same curve. The RNA pseudo-knots also can be represented as 2D graphical representations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

[1]  Bo Liao,et al.  Graphical approach to analyzing DNA sequences , 2005, J. Comput. Chem..

[2]  Tianming Wang,et al.  Analysis of similarity/dissimilarity of DNA sequences based on a condensed curve representation , 2005 .

[3]  Bo Liao,et al.  New 3D graphical representation of DNA sequences and their numerical characterization , 2003 .

[4]  EUGENE HAMORI,et al.  Novel DNA sequence representations , 1985, Nature.

[5]  Yu-Hua Yao,et al.  A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them , 2005, J. Comput. Chem..

[6]  Kequan Ding,et al.  A 4D representation of DNA sequences and its application , 2005 .

[7]  Bo Liao,et al.  A 3D Graphical Representation of RNA Secondary Structures , 2004, Journal of biomolecular structure & dynamics.

[8]  Bo Liao,et al.  New 2D graphical representation of DNA sequences , 2004, J. Comput. Chem..

[9]  T. Schlick,et al.  Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. , 2003, Nucleic acids research.

[10]  Bo Liao,et al.  Analysis of similarity/dissimilarity of DNA sequences based on 3-D graphical representation , 2004 .

[11]  Emanuele Paci,et al.  Membrane Crossing by a Polar Molecule: A Molecular Dynamics Simulation , 1994 .

[12]  R. Nussinov,et al.  Tree graphs of RNA secondary structures and their comparisons. , 1989, Computers and biomedical research, an international journal.

[13]  Kequan Ding,et al.  Application of 2-D graphical representation of DNA sequence , 2005 .

[14]  Dejan Plavšić,et al.  Novel 2-D graphical representation of DNA sequences and their numerical characterization , 2003 .

[15]  Tianming Wang,et al.  3-D graphical representation of DNA sequences and their numerical characterization , 2004 .

[16]  Kequan Ding,et al.  On A Six-Dimensional Representation of RNA Secondary Structures , 2005, Journal of biomolecular structure & dynamics.

[17]  E. Hamori,et al.  H curves, a novel method of representation of nucleotide series especially suited for long DNA sequences. , 1983, The Journal of biological chemistry.

[18]  A. Nandy.  A new graphical representation and analysis of DNA sequence structure. I: Methodology and application to globin genes , 1994 .

[19]  Milan Randic,et al.  On 3-D Graphical Representation of DNA Primary Sequences and Their Numerical Characterization , 2000, J. Chem. Inf. Comput. Sci..

[20]  Wen Zhu,et al.  Analysis of similarity between RNA secondary structures , 2005 .

[21]  M. A. GATES,et al.  Simpler DNA sequence representations , 1985, Nature.

[22]  Bo Liao.  A 2D graphical representation of DNA sequence , 2005 .