CINEMA - A NOVEL COLOR INTERACTIVE EDITOR FOR MULTIPLE ALIGNMENTS (REPRINTED FROM GENE, VOL 221, PG GC57-GC63, 1998)

CINEMA is a new editor for manipulating and generating multiple sequen ce alignments. The program provides both an interface to existing data bases of alignments on the Internet and a tool for constructing and mo difying alignments locally. It is written in Java, so executable code will run on most major desktop platforms without modification. The imp lementation is highly flexible, so the applet can be easily customised with additional functions; and the object classes are reusable, promo ting rapid development of program extensions. Formerly, such extended functionality might have been provided via browser plug-ins, which hav e to be downloaded and installed on every client before loading data. Now, for the first time, an applet is available that allows interactiv e client-side processing of an alignment, which can then be stored or processed automatically on the server. The program is embedded in a co mprehensive help file and is accessible both as a stand-alone tool on UCL's Bioinformatics Server: //www.biochem.ucl.ac.uk/bsm/dbbrowser/CIN EMA2.02/, and as an integral part of the PRINTS protein fingerprint da tabase. Exploitation of such novel technologies revolutionises the way users may interact with public databases in the future: bioinformatic s centres need not simply provide data, but are now able to offer the means by which information is visualised and manipulated, without the requirement for users to install software. (C) 1998 Elsevier Science B .V. All rights reserved.