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Non-quantized minimum free energy in untranslated region exons

conference contribution
posted on 2007-01-01, 00:00 authored by Keith Knapp, Ahadur Rahaman, Yi-Ping Phoebe Chen
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.



Institute of Electrical and Electronics Engineers. Conference (2007: Fremont, Calif.)


32 - 37


Institute of Electrical and Electronics Engineers


Fremont, Calif.

Place of publication

Los Alamitos, Calif.

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Publication classification

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.


X Chen, E Damiani, T Dillon, J He, J Gao, J Li, A Sidhu, M Song, I Yoo, X Zhou

Title of proceedings

Proceedings: 2007 IEEE International Conference on Bionformatics and Biomedicine Workshops

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