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I am currently looking at MongoDB and ArangoDB as the database for our web application, but neither appear to support cross-database joins, does anyone know if there is such a document database that supports this please?

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You can do it postgres

Update as of 9.3

You can now use the new postgres_fdw (foreign data wrapper) to connect to tables in any Postgres database - local or remote.

also you can use dblink functionality but it isn't part of the default PostgreSQL install, but you can add it in.- dblink.

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