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Lists of Software for
Bioinformatics: Visualization Tools
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[ D, E, F ] --
[ G, H, I ] --
[ J, K, L ]
[ M, N, O ] --
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[ S, T, U ] --
[ V, W ] --
[ X, Y, Z]
--- A, B, C ---
CLC Workbench is a freeware bioinformatics software package available for Windows, MacOS X and Linux. CLC Free Workbench integrates several features into one single user-friendly program.
--- D, E, F ---
--- G, H, I ---
--- J, K, L ---
KoriBlast is a reliable graphical environment dedicated to Blast data mining. KoriBlast combines Blast searches with advanced data management capabilities and a state-of-the-art graphical user interface.
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--- P, Q, R ---
Relibase is a web-based tool for searching and analysing protein ligand structures in the PDB. It features:
- An intuitive web-based user interface
- A fast database search engine
- Local installation for confidential searching
- Standard text searching
- 2D substructure searching
- 3D protein-ligand interaction searching
- Similarity searching for ligands
- Clear 3D visualisation using RasMol
- Automatic superposition of related binding sites to compare ligand binding modes, water positions, ligand-induced conformational changes, etc.
Relibase is freely available from http://relibase.ccdc.cam.ac.uk and the mirror sites http://relibase.rutgers.edu and http://relibase.ebi.ac.uk
More information about Relibase, and the commercial version Relibase+ is available from the CCDC website at http://www.ccdc.cam.ac.uk/prods/relibase/
--- S, T, U ---
SeqVerter from GeneStudio, Inc. (http://www.genestudio.com) is a free nucleotide sequence converter/viewer for Windows. Features include compatibility with most formats, including files imported from or exported to Mac and UNIX computers. Can be used for batch operations, melding of single sequence files into multiple sequence files, and extraction of single sequences from multiple sequence files. The program is very easy to use due to a drag-and-drop interface and a downloadable tutorial.
SimVector: Automates the production of publication quality graphics of vectors and provides sequence analysis to assist in the design of cloning experiments. For: Windows NT / 98 / 2000 / ME / XP and Mac OS X. Available from
PREMIER Biosoft International
3786 Corina Way
Palo Alto, CA 94303-4504
Phone: 650-856-2703
Fax: 650-843-1250
http://www.PremierBiosoft.com
--- V, W ---
VIBE (Visual Integrated Bioinformatics Environment). Introducing a next generation visualization and genomics discovery tool: the Visual Integrated Bioinformatics Environment (VIBE). Developed by INCOGEN in collaboration with TimeLogic Corporation, VIBE is a visual data analysis and mining environment designed specifically for the TimeLogic DeCypher platform. This new, highly sophisticated client/server system, combined with TimeLogic's powerful DeCypher accelerators, offers the bioinformatics researcher an unprecedented total and integrated solution to data mining and informatics discovery.
- Efficient drag-and-drop sequence analysis pipeline construction
- Visual implementation of all DeCypher algorithms
- Data filtering on simple or complex criteria
- Distributed, multi-user support
- Interactive or batch mode pipeline execution
- User editable representation of pipelines in XML and Perl
- State-of-the-art, interactive visualization tools
- Intuitive, user-friendly data representation
- Results accessible from active and previously completed pipelines
System Recommendations: VIBE is a client/server system requiring Unix or Windows as the workstation operating system and Unix as the server-side operating system. A TimeLogic DeCypher server is also needed to execute the sequence analysis algorithms. Contact:
- Incogen, Inc.
- 263 McLaws Circle
- Suite 200
- Williamsburg, VA 23185
- Phone: 800-286-6599
- Fax: 864-654-0887
- E-mail: info@incogen.com
Visual Cloning 2000 is an advanced new vector map drawing and sequence analysis program that includes the following features:
- Sophisticated graphics and extensive customization of genetic maps, including multiple maps per pa
- Extensive web integration, including fast and easy conversion from a GenBank or EMBL file to a graphical map, and integrated online ordering of enzymes and prime
- Advanced restriction analysis, with over 1000 enzymes
- Open Reading Frames sear
- PCR primer and hybridization oligonucleotide desi
- Sequence view
- Subsequence sear
- Intuitive user interface
The beta version of Visual Cloning 2000 is available for download at http://www.redasoft.com.
WHAT IF is an extensive protein modeling, protein structure analysis, database handler, molecular graphics package. It is available for all Evans & Sutherland equipment and Silicon Graphics machines. The program is supplied with source code, databases and documentation. Contact:
G. Vriend
E.M.B.L.
Meyerhofstrasse 2
D-6900 Heidelberg
GERMANY
Tel: +49-622-138-7473
Fax: +49-6221-387517
E-mail: VRIEND@EMBL-Heidelberg.de
URL:
http://www.cmbi.kun.nl/
The program is also available from Suhaib M. Siddiqi (ssiddiqi@inspirepharm.com) for Windows from the Inspire Pharmaceuticals Web page at http://www.inspirepharm.com/whatif