A class of 2D graphical representations of RNA secondary structures and the analysis of similarity based on them

Based on the concepts of cell and system of graphical representation, a class of 2D graphical representations of RNA secondary structures are given in terms of classifications of bases of nucleic acids. The representations can completely avoid loss of information associated with crossing and overlapping of the corresponding curve. As an application, we make quantitative comparisons for a set of RNA secondary structures at the 3′‐terminus of different viruses based on the graphical representations. The examination of similarities/dissimilarities illustrates the utility of the approach. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1339–1346, 2005

[1]  Jun Wang,et al.  Characteristic Sequences for DNA Primary Sequence , 2002, J. Chem. Inf. Comput. Sci..

[2]  C. Reusken,et al.  Structural elements of the 3'-terminal coat protein binding site in alfalfa mosaic virus RNAs. , 1996, Nucleic acids research.

[3]  S. Scott,et al.  The complete nucleotide sequence of prune dwarf ilarvirus RNA 3: implications for coat protein activation of genome replication in ilarviruses. , 1994, Virology.

[4]  Dejan Plavšić,et al.  Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation , 2003 .

[5]  E C Koper-Zwarthoff,et al.  Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus. , 1980, Nucleic acids research.

[6]  Yu-hua Yao,et al.  A class of new 2-D graphical representation of DNA sequences and their application , 2004 .

[7]  Milan Randic,et al.  On A Four-Dimensional Representation of DNA Primary Sequences , 2003, J. Chem. Inf. Comput. Sci..

[8]  M. Gates.  A simple way to look at DNA. , 1986, Journal of theoretical biology.

[9]  B Li,et al.  Creating chemical diversity to target protein kinases. , 2004, Combinatorial chemistry & high throughput screening.

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

[11]  A. Nandy,et al.  GRAPHICAL ANALYSIS OF DNA SEQUENCE STRUCTURE. II: RELATIVE ABUNDANCES OF NUCLEOTIDES IN DNAS, GENE EVOLUTION AND DUPLICATION , 1995 .

[12]  J. Bol,et al.  Complete nucleotide sequence of tobacco streak virus RNA 3. , 1984, Nucleic acids research.

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

[14]  S. Scott,et al.  The complete nucleotide sequence of RNA 3 of citrus leaf rugose and citrus variegation ilarviruses. , 1995, The Journal of general virology.

[15]  Chandan Raychaudhury,et al.  Indexing Scheme and Similarity Measures for Macromolecular Sequences , 1999, J. Chem. Inf. Comput. Sci..

[16]  C. D'arcy,et al.  The nucleotide sequence of apple mosaic virus coat protein gene has no similarity with other Bromoviridae coat protein genes. , 1994, The Journal of general virology.

[17]  W G Duddleson,et al.  Computer program sequence for analysis and summary of radioimmunoassay data. , 1972, Computers and biomedical research, an international journal.

[18]  Milan Randic.  Condensed Representation of DNA Primary Sequences , 2000, J. Chem. Inf. Comput. Sci..

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

[20]  S. Scott,et al.  The complete nucleotide sequence of the RNA 3 of lilac ring mottle ilarvirus. , 1995, The Journal of general virology.

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

[22]  K. Liem,et al.  Nucleotide sequence and structural determinants of specific binding of coat protein or coat protein peptides to the 3' untranslated region of alfalfa mosaic virus RNA 4 , 1994, Journal of virology.

[23]  P. Walstra,et al.  Nucleotide sequence of the 3'-noncoding region of alfalfa mosaic virus RNA 4 and its homology with the genomic RNAs. , 1979, Nucleic acids research.

[24]  Milan Randic,et al.  On the Similarity of DNA Primary Sequences , 2000, J. Chem. Inf. Comput. Sci..

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