BACKGROUND: The Ageing Factor Database AgeFactDB contains a large number of lifespan observations for ageing-related factors like genes, chemical compounds, and other factors such as dietary restriction in different organisms. These data provide quantitative information on the effect of ageing factors from genetic interventions or manipulations of lifespan. Analysis strategies beyond common static database queries are highly desirable for the inspection of complex relationships between AgeFactDB data sets. 3D visualisation can be extremely valuable for advanced data exploration. RESULTS: Different types of networks and visualisation strategies are proposed, ranging from basic networks of individual ageing factors for a single species to complex multi-species networks. The augmentation of lifespan observation networks by annotation nodes, like gene ontology terms, is shown to facilitate and speed up data analysis. We developed a new Javascript 3D network viewer JANet that provides the proposed visualisation strategies and has a customised interface for AgeFactDB data. It enables the analysis of gene lists in combination with AgeFactDB data and the interactive visualisation of the results. CONCLUSION: Interactive 3D network visualisation allows to supplement complex database queries by a visually guided exploration process. The JANet interface allows gaining deeper insights into lifespan data patterns not accessible by common database queries alone. These concepts can be utilised in many other research fields.

MOTIVATION: DiProGB is an easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph. They include motif and repeat searches as well as statistical analyses. DiProGB adds a new dimension to the common genome analysis approaches by taking into account the physical properties of DNA and RNA. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at http://diprogb.fli-leibniz.de, implemented in C++ and supported on MS Windows and Linux (using e.g. WineHQ).

SUMMARY: GenColors is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes, considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. The genome comparison tools determine, for example, best-bidirectional hits, gene conservation, syntenies and gene core sets. Swiss-Prot/TrEMBL hits allow annotations in an effective manner. To further support the annotation base-specific quality data can also be displayed if available. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and maintained. It has been efficiently used for Borrelia garinii and is currently applied to various ongoing genome projects. AVAILABILITY: Detailed information on GenColors is available at http://gencolors.imb-jena.de. Online usage of GenColors-based genome browsers is the preferred application mode. The system is also available upon request for local installation.

The program HBexplore is a new tool for identifying and analysing H-bonding patterns in biological macromolecules. It selects all potential H-bonds according to geometrical criteria. The H-bond table can then be subjected to further automatic or interactive analysis tools. These tools include the calculation of mean values and distributions of geometrical H-bond parameters for parts of a single structure, for complete single structures and for structure sets, the classification of each H-bond according to the participation of backbone, side chain or base, ligand and water parts of nucleic acids or proteins, identification of Watson-Crick nucleotide pairs and of H-bonded pairs of equal nucleotides, the calculation of the mean number of H-bonds per residue, and of the fraction of potential donor and acceptor atoms involved in H-bonds. HBexplore further generates automatically a H-bond residue interaction table. This table lists for all residues of the structure the other residues, ligands or water molecules directly connected via a H-bond. By means of a binary tree search algorithm, this table is then converted into a H-bond cluster table. Clusters are understood here as an uninterrupted network of H-bonded residues. For nucleic acids, secondary structures and tertiary interactions are automatically derived from the H-bonding pattern. HBexplore is applied to two example RNA structures: a pseudoknot and a hairpin. It provides a comprehensive listing of individual H-bonds and statistical information for larger structure sets. In addition, it can identify interesting new H-bond motifs. One example is a pentanucleotide base-base H-bond interaction motif in the RNA pseudoknot. HBexplore is intended to contribute both to the elucidation of general principles of the architecture of biological macromolecules, and to the prediction and refinement of single structures.

An Image Library of Biological Macromolecules is described, which contains image and text files related to structures of biological macromolecules. Currently, the Library has approximately 3000 image files of approximately 300 structures of biological macromolecules whose coordinates are available in the Protein Data Bank and in the Nucleic Acid Database. The entries include all RNA structures, approximately 70 DNA structures, 150 proteins and a few carbohydrates. The Library contains further images of amino acids, of standard and modified nucleotides and of nucleic acid model structures. Each entry consists of an annotation file with bibliographic and sequence information and possibly comments, of a color-coded distance plot and of structure images. Almost all of the images are available both in a mono and in a stereo representation. Standard procedures for generating these images were strictly avoided. Therefore, mixed rendering, coloring and labeling techniques were used extensively. Since May 1995 the Library has a growing division of images in the new Virtual Reality Modeling Language (VRML) format. The Image Library of Biological Macromolecules can be accessed via the World-Wide Web (http://www.imb-jena.de/IMAGE.html). There is a large number of structures determined by experimental and/or modeling techniques which are not intended to be included into the Protein Data Bank or Nucleic Acid Database for some reason. The Image Library could be a repository of these structures and of images of these and other structures of biological macromolecules including structures which are not known at atomic detail. Authors who are willing to make available images or coordinates to the scientific community via the Image Library of Biological Macromolecules are requested to contact the author.