Geneplot

AvV avvliet at ision.nl
Fri Jul 20 15:34:58 EST 2001


I don't know how the program works, but for bacteria it is easier to do
without. Just look whether there is an ATG / GTG / TTG startcodon, and a
AGGA / AAGG / AGAG /AGGG or other short AG sequence at approx 10 bp in front
of the gene. That corresponds to the ribosome binding site. Works most of
the time

hope this helps
Arnoud

"Sergio" <sergioal at bbm1.ucm.es> wrote in message
news:3B5874CE.BDC6C3EA at bbm1.ucm.es...
>
>
> Rafael Maldonado wrote:
>
> > Longe time I have used that program for the last time, but I think is a
> > kind of prediction of ORF by codon usage biass. The algorithms used for
> > this are basically two, one of them uses a table of preference for codon
> > usage, different for every organism and frame;
>
> i see, but what happens if there are a stop codon just in the middle of
those plateaus
> (policistronic messengers)? How does the program detect it's one big ORF
or some short
> ones?
> anyway, i still don't understand the advantage of using that approach for
finding
> ORFs... maybe in eucariotics organisms due to the presence of introns (and
therefore
> different codon composition i guess)... but in this case it was a
bacteria. However i
> have to say the graphic looks more "sophisticated" than the typical table
or drawing.
>
> thanks for your quick reply
> Sergio
>





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