(1) Dept. of Molecular Sciences, Pfizer Central Research, Sandwich,
Kent CT13 9NJ, UK;
(2) Cyberdynamics UK Ltd., 38 Lordsbury Field, Wallington, Surrey SM6 9PE, UK;
(3) Dept. of Biochemistry and Molecular Biology, University College London,
Gower Street, London WC1E 6BT, UK.
djps@pfizer.com; andrewpayne@globalnet.co.uk; michie@bsm.bioc.ucl.ac.uk; attwood@bsm.bioc.ucl.ac.uk
A novel viewer/editor for manipulating and generating multiple sequence alignments is described. The program has been designed to act both as an interface to existing databases of alignments on the Internet and as a tool for constructing and modifying alignments locally. It is written in the object oriented network programming language, Java. This is important as it means that executable code will run on almost all major desktop platforms without recompilation. The program, JavaCINEMA, is easy to use and has been embedded in a comprehensive help file. The implementation is highly flexible, so the applet can be customised with ease to plug in a range of additional functions. For example, we are developing a variety of `pluglets', including a structural viewer for those sequences for which 3D coordinates are available, and interfaces to a small-molecule database and to the Berkeley Genome Browser. The functionality that, together, we are implementing will render the applet an immensely powerful bioinformatics tool. JavaCINEMA is currently accessible via UCL's DbBrowser Bioinformatics server: http://www.biochem.ucl.ac.uk/bsm/dbbrowser/CINEMA/.