title: DNA sequence representation without degeneracy.
abstract: 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.
authors.affiliation: Department of Mathematics, Statistics and Computer Science, University of Illinois at Chicago, 851 South Morgan Street, Chicago, IL 60607-7045, USA. yau@uic.edu
authors.forename: Stephen S-T
authors.initials: SS
authors.lastname: Yau
authors.forename: Jiasong
authors.initials: J
authors.lastname: Wang
authors.forename: Amir
authors.initials: A
authors.lastname: Niknejad
authors.forename: Chaoxiao
authors.initials: C
authors.lastname: Lu
authors.forename: Ning
authors.initials: N
authors.lastname: Jin
authors.forename: Yee-Kin
authors.initials: YK
authors.lastname: Ho
mesh_terms: D000818:Animals; D001483:Base Sequence; D006801:Humans; D051379:Mice; D008962:Models, Theoretical; D017422:Sequence Analysis, DNA / Q000379:methods*