title: A physicochemical model for analyzing DNA sequences.
abstract: In search of an ab initio model to characterize DNA sequences as genes and nongenes, we examined some physicochemical properties of each trinucleotide (codon), which could accomplish this task. We constructed three-dimensional vectors for each double-helical trinucleotide sequence considering hydrogen-bonding energy, stacking energy, and a third parameter, which we provisionally identified with DNA-protein interactions. As this three-dimensional vector moves along any genome, the net orientation of the resultant vector should differ significantly for gene and nongene regions to make a distinction feasible, if the underlying model has some merits. An analysis of 331 prokaryotic genomes comprising a total of 294 786 experimentally verified genes (nonoverlapping) and an equal number of nongenes presents a proof of concept of the model without the need for further parametrization. Also, initial analyses on Saccharomyces cerevisiae and Arabidopsis thaliana suggest that the methodology is extendable to eukaryotes. The physicochemical model (ChemGenome1.0) introduced has the potential to be developed into a gene-finding algorithm and, more pressingly, could be employed for an independent assessment of the annotation of DNA sequences.
authors.affiliation: Department of Chemistry and Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi.
authors.forename: Samrat
authors.initials: S
authors.lastname: Dutta
authors.forename: Poonam
authors.initials: P
authors.lastname: Singhal
authors.forename: Praveen
authors.initials: P
authors.lastname: Agrawal
authors.forename: Raju
authors.initials: R
authors.lastname: Tomer
authors.forename: Kritee
authors.initials: K
authors.lastname: Kritee
authors.forename: Ekta
authors.initials: E
authors.lastname: Khurana
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D016680:Genome, Bacterial; D008956:Models, Chemical
chemical_list: D004247:DNA