Mapper with annotation support

[dbrami]

I am looking for a mapping software that can handle Genbank formatted files as input.
I plan on mapping 454 cDNA reads back to this reference so mappers that work on short reads exclusively are disqualified.
The best option I have so far is using CLC Bio but i won't tell me the locations of hits if a read maps to multiple places.
I would also love to expression values and the RNASeq tool in CLC will only map to coding regions. I am curious about intergenic regions.
Bummer...

Does anyone have any suggestions?

[dbrami]

PS: I would love to be able to BLAST a db of annotations to my single pseudomolecule but BLAST only accepts FASTA or SN.1 files...