Sounds like Advent Rising. Excellent game, but rather disappointing that it was made as the first part of a trilogy, the two last chapters of which were never made. For some reason, lots of people here have said how much they hate it. I found it very much like Mass Effect 1, both in style and quality.
I played Advent Rising and had a blast, but I wouldn't hold it up to Mass Effect for a second. For one thing, Bioware does characters and story better than most -- Advent, on the other hand, felt to me like it was best enjoyed on MST3K terms.
The most enjoyable moment in that game, IIRC, was during Gideon's training montage when I alt-tabbed out of the game to blast the Team America montage song
in the background. Honestly, the game was worth it just for that.