Non-quantized minimum free energy in untranslated region exons

Knapp, Keith, Rahaman, Ahadur and Chen, Yi-Ping Phoebe 2007, Non-quantized minimum free energy in untranslated region exons, in Proceedings: 2007 IEEE International Conference on Bionformatics and Biomedicine Workshops, Institute of Electrical and Electronics Engineers, Los Alamitos, Calif., pp. 32-37.

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Title Non-quantized minimum free energy in untranslated region exons
Author(s) Knapp, Keith
Rahaman, Ahadur
Chen, Yi-Ping Phoebe
Conference name Institute of Electrical and Electronics Engineers. Conference (2007: Fremont, Calif.)
Conference location Fremont, Calif.
Conference dates 2-4 Nov 2007
Title of proceedings Proceedings: 2007 IEEE International Conference on Bionformatics and Biomedicine Workshops
Editor(s) Chen, Xue-Wen
Damiani, Ernesto
Dillon, Tharam S.
He, Jing
Gao, Jean
Li, Jinyan
Sidhu, Amandeep S.
Song, Min
Yoo, Illhoi
Zhou, Xiaohua
Publication date 2007
Conference series IEEE/ACIS International Conference on Computer and Information Science
Start page 32
End page 37
Publisher Institute of Electrical and Electronics Engineers
Place of publication Los Alamitos, Calif.
Summary In an attempt to improve automated gene prediction in the untranslated region of a gene, we completed an in-depth analysis of the minimum free energy for 8,689 sub-genetic DNA sequences. We expanded Zhang's classification model and classified each sub-genetic sequence into one of 27 possible motifs. We calculated the minimum free energy for each motif to explore statistical features that correlate to biologically relevant sub-genetic sequences. If biologically relevant sub-genetic sequences fall into distinct free energy quanta it may be possible to characterize a motif based on its minimum free energy. Proper characterization of motifs can lead to greater understanding in automated genefinding, gene variability and the role DNA structure plays in gene network regulation.

Our analysis determined: (1) the average free energy value for exons, introns and other biologically relevant sub-genetic sequences, (2) that these subsequences do not exist in distinct energy quanta, (3) that introns exist however in a tightly coupled average minimum free energy quantum compared to all other biologically relevant sub-genetic sequence types, (4) that single exon genes demonstrate a higher stability than exons which span the entire coding sequence as part of a multi-exon gene and (5) that all motif types contain a free energy global minimum at approximately nucleotide position 1,000 before reaching a plateau. These results should be relevant to the biochemist and bioinformatician seeking to understand the relationship between sub-genetic sequences and the information behind them.
ISBN 9781424416042
Language eng
Field of Research 080199 Artificial Intelligence and Image Processing not elsewhere classified
HERDC Research category E1 Full written paper - refereed
Copyright notice ©2007 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution to servers or lists, or to reuse any copyrighted component of this work in other works must be obtained from the IEEE.
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