title: A novel method for prokaryotic promoter prediction based on DNA stability.
abstract: 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 seems to provide a much better clue than usual sequence motifs, such as Pribnow box and -35 sequence, for differentiating promoter region from non-promoter regions. To a certain extent, it is more general and is likely to be applicable across organisms. Hence incorporation of such features in addition to the signature motifs can greatly improve the presently available promoter prediction programs.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India. aditi@mbu.iisc.ernet.in <aditi@mbu.iisc.ernet.in>
authors.forename: Aditi
authors.initials: A
authors.lastname: Kanhere
authors.forename: Manju
authors.initials: M
authors.lastname: Bansal
mesh_terms: D020816:Amino Acid Motifs; D001412:Bacillus subtilis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D048230:Corynebacterium glutamicum / Q000235:genetics; D004247:DNA / Q000737:chemistry*; D004926:Escherichia coli / Q000235:genetics; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D015233:Models, Statistical; D011401:Promoter Regions, Genetic; D012313:RNA / Q000737:chemistry; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013816:Thermodynamics; D014158:Transcription, Genetic
chemical_list: D012313:RNA; D004247:DNA