title: DNA-energetics-based analyses suggest additional genes in prokaryotes.
abstract: We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.
authors: Department of Chemistry, Kusuma School of Biological Sciences, Indian Institute of Technology,  New Delhi 110 016, India.
authors: Garima
authors: G
authors: Khandelwal
authors: Jalaj
authors: J
authors: Gupta
authors: B
authors: B
authors: Jayaram
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D006860:Hydrogen Bonding; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D045704:Mycoplasma genitalium / Q000235:genetics; D016366:Open Reading Frames; D017422:Sequence Analysis, DNA; D044366:Transition Temperature
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial