Condensed Representation of DNA Primary Sequences

With rapid reporting of DNA sequences derived from automated DNA sequencing techniques, the problem of reviewing and ordering such information has become acute. We have introduced a condensed representation of primary sequences of DNA that offers an alternative method of registering DNA. The advantage of the condensed codes for DNA is that it not only offers fast, qualitative comparisons of DNA but also allows quantitative comparisons of DNA from different sources. The approach is outlined for a particular human beta globin sequence extract. Using the condensed representation of the primary DNA sequences, comparisons are made between primary sequences for Exon 1 of human beta globin and seven other beta globins.

[1]  Milan Kunz,et al.  Distributions of Distances in Information Strings , 1998, J. Chem. Inf. Comput. Sci..

[2]  Y. K. Huen.  Representation of Biological Sequences Using Point Geometry Analysis , 1995 .

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

[4]  Ping-an He,et al.  Numerical Characterization of DNA Primary Sequence , 2002 .

[5]  Eduardo Mizraji,et al.  Perceptible Features in Graphical Representations of Nucleic Acid Sequences , 1995 .

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

[7]  H Herzel,et al.  The modular structure of informational sequences. , 1996, Bio Systems.

[8]  Milan Randić,et al.  On characterization of DNA primary sequences by a condensed matrix , 2000 .

[9]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[10]  Milan Randić,et al.  On the Characterization of Fullerenes , 1994 .

[11]  Frank Harary,et al.  Toward a General Calculus of Phonemic Distribution , 1957 .

[12]  J. Kruskal.  An Overview of Sequence Comparison: Time Warps, String Edits, and Macromolecules , 1983 .

[13]  M. Randic,et al.  Comparison of sequences as a method for evaluation of the molecular similarity , 1986, Journal of computational chemistry.

[14]  A. Nandy.  GRAPHICAL ANALYSIS OF DNA SEQUENCE STRUCTURE : III. INDICATIONS OF EVOLUTIONARY DISTINCTIONS AND CHARACTERISTICS OF INTRONS AND EXONS , 1996 .