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Nucleic Acids Research, 2003, Vol. 31, No. 12 3078-3080
© 2003 Oxford University Press

DNA sequence representation without degeneracy

Stephen S. -T. Yau, Jiasong Wang1, Amir Niknejad, Chaoxiao Lu, Ning Jin1 and Yee-Kin Ho2

Department of Mathematics, Statistics and Computer Science and 2 Department of Biochemistry and Molecular Biology, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7045, USA and 1 Department of Mathematics, Nanjing University, Nanjing 210008, China

*To whom correspondence should be addressed. Tel/Fax: +1 312 996 3065; Email: yau{at}uic.edu

Graphical representation of DNA sequence provides a simple way of viewing, sorting and comparing various gene structures. A new two-dimensional graphical representation method using a two- quadrant Cartesian coordinates system has been derived for mathematical denotation of DNA sequence. The two-dimensional graphic representation resolves sequences’ degeneracy and is mathematically proven to eliminate circuit formation. Given x-projection and y-projection of any point on the graphical representation, the number of A, G, C and T from the beginning of the sequence to that point could be found. Compared with previous methods, this graphical representation is more in-line with the conventional recognition of linear sequences by molecular biologists, and also provides a metaphor in two dimensions for local and global DNA sequence comparison.


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