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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.

SUBMITTER: Yau SS

PROVIDER: S-EPMC162336 | biostudies-literature | 2003 Jun

REPOSITORIES: biostudies-literature

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DNA sequence representation without degeneracy.

Yau Stephen S-T SS Wang Jiasong J Niknejad Amir A Lu Chaoxiao C Jin Ning N Ho Yee-Kin YK

Nucleic acids research 20030601 12

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 representa ...[more]

PMID: 12799435

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