Vol. 9, Issue 3, 277-281, March 1999

METHODS
DNA Sequence Chromatogram Browsing Using JAVA and CORBA

¹ EMBL-OutstationThe European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; ² Department of Computer and Information Science University of Pennsylvania, Philadelphia, Pennsylvania 19104 USA; ³ Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri 63108 USA

DNA sequence chromatograms (traces) are the primary data source for all large-scale genomic and expressed sequence tags (ESTs) sequencing projects. Access to the sequencing trace assists many later analyses, for example contig assembly and polymorphism detection, but obtaining and using traces is problematic. Traces are not collected and published centrally, they are much larger than the base calls derived from them, and viewing them requires the interactivity of a local graphical client with local data. To provide efficient global access to DNA traces, we developed a client/server system based on flexible Java components integrated into other applications including an applet for use in a WWW browser and a stand-alone trace viewer. Client/server interaction is facilitated by CORBA middleware which provides a well-defined interface, a naming service, and location independence.

[The software is packaged as a Jar file available from the following URL: http://www.ebi.ac.uk/~jparsons. Links to working examples of the trace viewers can be found at http://corba.ebi.ac.uk/EST. All the Washington University mouse EST traces are available for browsing at the same URL.]