cDNA alignment software: seeking

[Kerry Rowe]

Newsgroups: bionet.software
Subject: seeking: cDNA alignment software
Summary: 
Expires: 
Sender: 
Followup-To: 
Distribution: bionet.molbio.genome-program, bionet.software.sources
Organization: University of Utah Computer Center, Salt Lake City, Ut.
Keywords: 
Cc: 
I'm looking for a particular type of DNA alignment software. What I 
need is to align cDNA with genomic DNA. The alignment software would
need to either split the cDNA into the fragments (e.g., exons) that
are homologous with sections of the genomic DNA and then align these, 
or the software could simply present multiple alignments. Some software
packages, such as CAP, do a good job for contig assembly, but do not
handle the special case I describe above. 

Does any software like this exist already? If so, how do I obtain it?
Any help would be appreciated.

Steve Bayer

please respond to: bayer at darwin.med.utah.edu