comparing sequences and mapping annotations?

[gaster]

We have two sequences with a little divergence and no large-scale rearrangments (ie gene order and number are probably maintained). One sequence is already annotated. We are trying to find a way to just map the annotations of one onto the other (then we would just proof it by hand). It seems like it should be easy but no programs that we can find allow it. For instance, although Mauve will align the two sequences, the output file only lists the annotation coordinates of the reference sequence (not the new sequence).

Any ideas? Has anyone done something like this comparing and annotating different strains.

Any help is mightily appreciated!