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Nucleic Acids Res. 2003 Jun 15;31(12):3078-80.

DNA sequence representation without degeneracy.

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  • 1Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7045, USA.


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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