GMV (Genome Map Viewer) is a tool that compares gene order in two or more genomes and displays the results in the form of the concentric ring display of Moore et al.(1995) and Gale and Devos (1998). This display shows the relative positions of linkage blocks in a set of species, where these blocks have been proposed on the basis of conservation of gene order across the species being examined. In cereals these blocks are often based on rice.
Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH. CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.
PrIMETV is a program that can visualize tree-within-tree phenomena such as gene/species tree reconciliations. Output can be given in a range of formats.
Antheprot 3D is a molecular graphics program intended for the visualisation of proteins, nucleic acids from RCSB archive. The program is aimed at display, teaching and generation of publication quality images.
The program reads in a molecule coordinate file (PDB format) and interactively displays the molecule on the screen in a variety of color schemes and molecule representations. Currently available representations include wireframes, sticks, spheres, ball and stick, atom labels and distances. PDB files that are available either locally (Ctrl+O or File=>Open) or distantly at “POLE Bioinformatique Lyonnais” (Ctrl+I) or File=> PBIL URL can be loaded directly into AntheProt3D.
The program is made of 3 different windows:
A 3D view window which allows the user to interactively move the molecule
A group selection panel for group selection
A text window for provinding the user the list of clicked atoms, information (F2) and PHI, PSI values
A Ramachandran interactive plot is also available
Features
Alpha trace, wireframe, space filled,Balla nd Sticks, Sticks and surface mode.
Full support of clipping (“molecule slicing”)
Full support of stereo (side by side, anaglyph or quad buffer stereo)
Interactive Ramachandran plot
Hydrogen addition or removal by reduce
Selection of amino acids by group, chain or within a sphere
Surface viewer for MSMS files (Sanner, M.F., Spehner, J.-C., and Olson, A.J. (1996).Biopolymers, 38 (3), 305-320.
Ribbon or cylinder mode from Molscript program (P. J. Kraulis, (1991) Journal of Applied Crystallography 24, pp 946-950.)
Support for Delphi electrostatic potential Rocchia, W.; Alexov, E.; Honig, B. (2001) J Phys. Chem. 105, 6507-6514
If you use ANTHEPROT on PC, please cite one of the following references :
Deleage G, Combet C, Blanchet C, Geourjon, C
ANTHEPROT: An integrated protein sequence analysis software with client/server capabilities?
(2001) COMPUTERS IN BIOLOGY AND MEDICINE 31 (4): 259-267
Chemis3D is a Java Applet which renders virtual 3D molecular models within a Web document. It is specially designed for open interactive molecular visualization on the Internet or via an intranet. Molecular structures can be manipulated in real-time and rendered in various styles and appearances.
Chemis3D is a small applet running well on any Java-enabled browser and requiring no specialized plug-in nor professional applications.
Features
Real-time manipulation and fast 3D rendering.
Wide variety of molecular representations including special styles and color coding schemes for proteins and nucleic acids .
Enhanced interface using popumenu and key shortcuts .
Multi-models display and molecular animation capabilities.
Measuring and analysing tools.
Support of the most popular molecular data formats :Brookhaven Protein DataBank (*.pdb).MSC XMol files (*.xyz).MDL molfiles (*.mol).