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Indexing and configuring other databases

Many institutions may have local databases set up in their own Laboratory Information Management System. EMBOSS provides a simple mechanism for interfacing with such systems.

As long as a program is available that can be called noninteractively and returns the specified sequence on standard output, EMBOSS can interface with it. Use method: app or external (the two are equivalent) and app: "program command". The ID given in the USA will be appended to the command used to run the program. It is probably best to specify the methods available using the method subsets, methodall:, methodquery: and methodsingle: rather than using the generic method: tag.

Peter Rice 2007-04-26