A novel method for prokaryotic promoter prediction based on DNA stability

Background: In the post-genomic era, correct gene prediction has become one of the biggest challenges in genome annotation. Improved promoter prediction methods can be one step towards developing more reliable ab initio gene prediction methods. This work presents a novel prokaryotic promoter prediction method based on DNA stability. Results: The promoter region is less stable and hence more prone to melting as compared to other genomic regions. Our analysis shows that a method of promoter prediction based on the differences in the stability of DNA sequences in the promoter and non-promoter region works much better compared to existing prokaryotic promoter prediction programs, which are based on sequence motif searches. At present the method works optimally for genomes such as that of Escherichia coli, which have near 50 % G+C composition and also performs satisfactorily in case of other prokaryotic promoters. Conclusions: Our analysis clearly shows that the change in stability of DNA ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Aditi Kanhere, Manju Bansal
• Keywords: BMCBI 2005, Prokaryotic Promoter Prediction, Promoter Prediction, Promoter Prediction Method