Computing DNA duplex instability profiles efficiently with a two-state model: trends of promoters and binding sites

Background: DNA instability profiles have been used recently for predicting the transcriptional start site and the location of core promoters, and to gain insight into promoter action. It was also shown that the use of these profiles can significantly improve the performance of motif finding programs. Results: In this work we introduce a new method for computing DNA instability profiles. The model that we use is a modified Ising-type model and it is implemented via statistical mechanics. Our linear time algorithm computes the profile of a 10,000 base-pair long sequence in less than one second. The method we use also allows the computation of the probability that several consecutive bases are unpaired simultaneously. This is a feature that is not available in other linear-time algorithms. We use the model to compare the thermodynamic trends of promoter sequences of several genomes. In addition, we report results that associate the location of local extrema in the instability profiles w...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Miriam R. Kantorovitz, Zoi Rapti, Vladimir Gelev, Anny Usheva
• Keywords: BMCBI 2010, Business, Core Promoter, Core Promoter Element, Instability