I'm looking for a triple store to use with Java EE.
I ended with 2 possibilities, 4Store and Sesame but can't see the real difference between the two in term of features. I don't mind about performances details.
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I can't give you a full list of features for either tool, but I reckon that an important difference for your use case (given what little you've told us) is that wile 4Store is an RDF database implementation (or "triplestore"), Sesame is a framework API for handling RDF in Java, giving access to multiple triplestore implementations (including some of its own, but also many third-party products). The possible advantage of this is that it allows you switching to a different database (if you so require) without major changes to your code.
I would also imagine that Sesame's API, being developed in and for Java, is slightly more feature-rich and easy to use in a Java EE environment, but this is merely an assumption as I am not sufficiently familiar with 4Store to make an actual comparison.
(disclosure: I am on the Sesame development team)