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>

> 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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