Biology – Quantitative Biology – Biomolecules
Scientific paper
2008-06-12
J. Phys.: Condens. Matter 21 (2009) 034109
Biology
Quantitative Biology
Biomolecules
17 pages, 8 figures; new introduction, added refs, minor changes
Scientific paper
10.1088/0953-8984/21/3/034109
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main challenges include the difficulty of mathematically mapping a qualitative description of DNA melting domains to quantitative statistical mechanics models, as well as the absence of 'gold standards' and a need for generality. In this paper, we introduce a new approach to identify the twostate regions and melting fork regions along a given DNA sequence. Compared with an ad hoc segmentation used in one of our previous studies, the new algorithm is based on boundary probability profiles, rather than standard melting maps. We demonstrate that a more detailed characterization of the DNA melting domain map can be obtained using our new method, and this approach is independent of the choice of DNA melting model. We expect this work to drive our understanding of DNA melting domains one step further.
Hovig Eivind
Liu Fang
Sandve Geir Kjetil
Tøstesen Eivind
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