Exon Mapping

Jerry Learn learn at u.washington.edu
Tue Jul 1 11:44:27 EST 1997


Well, it worked for me, but not quite the way that it was described. 

In article <33B42D95.41C6 at gcg.com>, Steve Smith <steve at gcg.com> wrote:

> 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.

Seqlab behaved exactly as described to this point.

> 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.

With Motif/CDE control-clicking rather than shift-clicking selects a
discontinuous set of CDS features.  (Shift-clicking selects a contiuous
set.) 

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

Here's where I had the problem: I got a single line of translation, all in
the reading frame of the first CDS.  If I select each CDS separately and
translate it (remembering to select align translation each time -- why
isn't this the default?), it works.
 
Despite my quibbles, this is a very useful feature for seqlab.  I enjoy
using it... I may someday even abandon GDE.




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