Exon Mapping

[Mr. A Guffanti]

Hi.

>Given protein sequence (e.g. from SwissProt), how do I:
>1) Trace the genomic sequence? Problem: usually I cannot find it, rather
>I come up with a cDNA. I do not actually need the intron information,
>but I do need to know where an exon begins and ends on the cDNA
>sequence.
>2) Map the above information automatically to my protein sequence.
>I have GCG v9.0, and WWW access. My platform is a Silicon-Graphics Indy.
>Any comment would be useful.

I found useful to solve similar problems the coupling of two freely-available programs
called "DPS" and "NAP". You can try them out at http://gcg.tigem.it/cgi-bin/dps.pl
and see if they can solve your problem at least in part, then ask them 
directly to the author !

Maybe I am naive, but you can solve this problem also with GCG FrameAlign,
setting the gap opening penalty to a suitable high penalty and gap extension to 
0 .. give it a try ! ..


                                 Ciao,

                                 Alessandro Guffanti
     

____________________________________________

Alessandro Guffanti
Informatics Core
Telethon Institute of Genetics and Medicine
c/o DIBIT - Via Olgettina, 58
20132 Milano - Italy
Tel.: +39-2-21560.212
Fax: +39-2-21560.220
email: guffanti at tigem.it
___________________________________________