This has been a feature of AfterEffects for as long as I can remember.  Years ago it was only JPEG sequences, but CS4 - CS5 imports PNG sequences which support transparent backgrounds and offer readymade Alpha channels.

I just finished an animated sequence of a robot walking that had massive motion blur and the composite in AfterEffects worked perfectly.  I just laid in the clip over the background footage, no need to key or mess with anything.  The transparency of the motion blurs came through beautifully.

 

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