Exon Mapping

Steve Smith steve at gcg.com
Fri Jun 27 16:16:05 EST 1997

Iddo Friedberg wrote:
> Hi,
> I'm looking for an elegant (failing that, feasable) method to map
> genomic sequences to
> protein sequences. The net result should look something like this:
> Genomic: -------++++++-----------+++++++++++-----++++++
> Protein:        ******           ***********     ******
> Where the "+" are exon codons, "-" intron codons, and "*" amino-acids.

Since you have version 9 of the GCG package:

1. Start SeqLab in editor mode

   seqlab -mode=editor 

2. Load the DNA sequence from Genbank/Embl

   File->Add Sequences Databases
   GenBank:L29190   (for example)
   Add to editor

3. Switch the display to Graphic Features, and scale the screen
   to 64 to 1.  Note the introns and exons.  This step is optional,
   but shows what is going on.

4. Double click on an exon to bring up the features window
   and show all features in the current sequence.

5. Select all of the features labeled CDS by clicking, and/or
   shift clicking on them.  You will note that the exons are
   selected in the Editor.

6. Edit->Translate, turn on Align Translation, and hit OK.

Your new sequence is created under the original.  Switch the
Display and scale back to normal and work on your new sequence.
If your sequence is not in the database, but is user derived,
then you will have to add the exon features before translating.

Hope this helps

Steve Smith
steve.smith at gcg.com

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