Exon Mapping

Marc Champagne M.Champagne at cellbio.duke.edu
Mon Jun 30 08:41:07 EST 1997


We are in the process of setting up a www page that will run a program that
allows the plotting of the codon bias of a sequence for a given organism.
It doesn't not pull out every coding region, but most often will.

We now have it running on unix, but have never tried exporting it.  

m.champagne at cellbio.duke.edu


-----
In article <5p05md$ea0 at net.bio.net>, Iddo Friedberg <idoerg at cc.huji.ac.il>
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.
> 
> Naturally, the data can appear as a mapping table, or anything else
> which is parseable.
> 
> 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.
> 
> Many thanks,
> 
> Iddo
> 
> --
> 
> Iddo Friedberg
> Phone: (972)-2-6758647
> email: idoerg at cc.huji.ac.il
> web: http://www.ls.huji.ac.il/~idoerg
> More info: finger idoerg at cc.huji.ac.il




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