ABSTRACT
Most of biologists work on textual DNA sequences that are limited to the linear representation of DNA. In this paper, we address the potential offered by Virtual Reality for 3D modeling and immersive visualization of large genomic sequences. The representation of the 3D structure of naked DNA allows biologists to observe and analyze genomes in an interactive way at different levels. We developed a powerful software platform that provides a new point of view for sequences analysis: ADNViewer. Nevertheless, a classical eukaryotic chromosome of 40 million base pairs requires about 6 Gbytes of 3D data. In order to manage these huge amounts of data in real-time, we designed various scene management algorithms and immersive human-computer interaction for user-friendly data exploration. In addition, one bioinformatics study scenario is proposed.
Subject(s)
Computational Biology , Imaging, Three-Dimensional , Nucleic Acid Conformation , Sequence Analysis, DNA , Algorithms , Base Sequence , Computational Biology/instrumentation , Computational Biology/methods , Humans , Imaging, Three-Dimensional/instrumentation , Imaging, Three-Dimensional/methods , Models, Molecular , Molecular Sequence Data , Sequence Analysis, DNA/instrumentation , Sequence Analysis, DNA/methods , SoftwareABSTRACT
MOTIVATION: Biologists usually work with textual DNA sequences (succession of A, C, G and T). This representation allows biologists to study the syntax and other linguistic properties of DNA sequences. Nevertheless, such a linear coding offers only a local and a one-dimensional vision of the molecule. The 3D structure of DNA is known to be very important in many essential biological mechanisms. By using 3D conformation models, one is able to construct a 3D trajectory of a naked DNA molecule. From the various studies that we performed, it turned out that two very different textual DNA sequences could have similar 3D structures. RESULTS: In this article, we address a new research work on 3D pattern matching for DNA sequences. The aim of this work is to enhance conventional pattern matching analyses with 3D-augmented criteria. We have developed an algorithm, based on 3D trajectories, which compares angles formed by these trajectories and thus quantifies the difference between two 3D DNA sequences. This analysis performs from a global scale to al local one. AVAILABILITY: Available on request from the authors.
Subject(s)
Algorithms , DNA/chemistry , DNA/ultrastructure , Models, Chemical , Models, Molecular , Sequence Analysis, DNA/methods , Base Sequence , Computer Simulation , Imaging, Three-Dimensional , Molecular Sequence Data , Nucleic Acid ConformationABSTRACT
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.
