Behind its spatial organization, the DNA's molecule conceals a rich functional reality. As a result, the study of the DNA's organization is increasingly attracting scientists. However, researches conducted until now are either local, or global but based on approximations and predictions that make the obtained model less credible. On the other hand, further researches on chromosomes' organization have identified some data and models representing, each one, a part of this organization. Our work aims to find a 3D repesentation that is global and more credible of the DNA's molecule. The molecule will be represented at the chromatin fiber level by means of 3D modeling algorithms. Initially, we have identified the biophysical data to be exploited. Indeed, we will first rely on the biophysical data of the chromatin fiber's structure as the persistence length along with the diameter, the confined volume and the curvature energy in order to build a first simple model of the chromatine.

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.

Many databases and software tools are available for biologists in order to have access to genomic information. In a SQL manner, our information system GenoMEDIA addresses the problem of integrating heterogeneous data-bases and software utilities within a generic distributed platform. Lysa increases the GenoMEDIA SQL interface by adding an interactive collaborative graphical environment. Upon a usual query on biological database, gigabytes of data could be returned to the users. The aim of Lysa, through the databall concept, a certain kind of data introspection and collaborative engine, is to allow groups of users to make semantic links in these huge amounts of data. The main point of this paper is the collaborative framework written for Lysa. This framework allows multiple users to work upon the same shared biological data. This was written in order to add the capabilities and the knowledge of multiple users in order to extract information of the huge mass of data coming from biological databases.

Many databases and software tools are currently available for accessing genomic data. In general, each tool uses a different type of data in exchange protocols, and usually they offer specific services. The presented system approach, named GenoMEDIA, addresses the problem of integrating these heterogeneous databases and software utilities within a generic distributed platform. GenoMEDIA provides two specific middleware, named Lydia and Antje, for this integration. Lydia offers facilities for working simultaneously with a variety of services and databases; Antje is designed to allow users to manage multiple heterogeneous remote databases in a uniform vision. The aim of this paper is to present GenoMEDIA and how heterogeneous databases and remote services are integrated, in particular how Antje was designed, implemented and tested with various genomic databases.