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
