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Determining promoter location based on DNA structure first-principles calculations

J Ramon Goñi123, Alberto Pérez12, David Torrents45 and Modesto Orozco146*

Author Affiliations

1 Institute for Research in Biomedicine, Parc Científic de Barcelona, Josep Samitier, Barcelona 08028, Spain

2 Departament de Bioquímica i Biología Molecular, Facultat de Biología, Avgda Diagonal, Barcelona 08028, Spain

3 Grup de recerca en Bioinformàtica i Estadística Mèdica, Departament de Biologia de Sistemes, Universitat de Vic. Laura, 13 08500 VIC, Spain

4 Computational Biology Program, Barcelona Supercomputer Center, Jordi Girona, Edifici Torre Girona, Barcelona 08028, Spain

5 Institut Català per la Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys, 23. Barcelona 08010, Spain

6 Instituto Nacional de Bioinformática, Structural Bioinformatics Unit, Parc Cientific de Barcelona, Josep Samitier, Barcelona 08028, USA

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Genome Biology 2007, 8:R263  doi:10.1186/gb-2007-8-12-r263

Published: 11 December 2007

Abstract

A new method for the prediction of promoter regions based on atomic molecular dynamics simulations of small oligonucleotides has been developed. The method works independently of gene structure conservation and orthology and of the presence of detectable sequence features. Results obtained with our method confirm the existence of a hidden physical code that modulates genome expression.