title: Representation and processing of complex DNA spatial architecture and its annotated genomic content.
abstract: This paper presents a new general approach for the spatial representation and visualization of DNA molecule and its annotated information. This approach is based on a biological 3D model that predicts the complex spatial trajectory of huge naked DNA. With such modeling, a global vision of the sequence is possible, which is different and complementary to other representations as textual, linguistics or syntactic ones. The DNA is well known as a three-dimensional structure. Whereas, the spatial information plays a great part during its evolution and its interaction with the other biological elements This work will motivate investigations in order to launch new bioinformatics studies for the analysis of the spatial architecture of the genome. Besides, in order to obtain a friendly interactive visualization, a powerful graphic modeling is proposed including DNA complex trajectory management and its annotated-based content structuring. The paper describes spatial architecture modeling, with consideration of both biological and computational constraints. This work is implemented through a powerful graphic software tool, named ADN-Viewer. Several examples of visualization are shown for various organisms and biological elements.
authors.affiliation: Gesture and Image group, LIMSI-CNRS, Université Paris-Sud, BP 133, F-91403 Orsay, France. gherbi@limsi.fr
authors.forename: Rachid
authors.initials: R
authors.lastname: Gherbi
authors.forename: Joan
authors.initials: J
authors.lastname: Herisson
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics; D015870:Gene Expression; D016678:Genome; D006678:HIV / Q000235:genetics; D017017:Methanococcus / Q000235:genetics; D008957:Models, Genetic; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012441:Saccharomyces cerevisiae / Q000235:genetics*
chemical_list: D004247:DNA