Geneplot

Sergio sergioal at bbm1.ucm.es
Fri Jul 20 13:13:34 EST 2001



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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