Genes and the physics of the DNA double-helix. formulation of a physics-based gene identification (PBGI) method: ab initio identification of genes in eukaryotic genomes

摘要

Method for the identification of genes and genetic signals based on the structural properties of DNA double-helix comprising the following steps: A-using the classical physical model of helix-coil transitions, B-calculating stability curves (probabilities of opening of the DNA double-helix, along a given sequence) by algorithmic methods), C-determining the disruption in the linear DNA for different temperatures, D-analyzing the stability curves for the detection of genetic signals (disruption of the double-helix) or the identification of coding regions (simple genes or exons in split genes as regions of high thermal stability), and optionally, E-based on the structural informations, performing classical sequence analysis (donor/acceptor sites, start and codon stops, in correspondence with the frontiers identified in the stability curves and open reading frames analyses) for completing the identification of genes.