finding introns and extrons

Allen Gathman agathman at semo.edu
Fri May 23 10:29:35 EST 2003


"OKL" <ongkl319 at hotmail.com> wrote in message news:<b9ghf2$250n$1 at justice.itsc.cuhk.edu.hk>...
> I'm an undergraduate student. I want to ask if i have a eukaryotic DNA or
> protein sequence, how can i find the no. of introns and extrons in the gene?
> e.g. by which software or computer program or which website

There are lots of ways.  One would be to go to NCBI and use ORF
finder, which gives some hint at least of where the coding regions are
in the gene.
http://www.ncbi.nlm.nih.gov/gorf/gorf.html

However, this won't find all the intron splice junctions, just show
you where there are open reading frames that COULD be exons.  You can
try GlimmerM's online server, which will find exons in a DNA sequence.
 It works particularly well for the species they've trained it for
(see list on web site), and may work adequately for others.

http://www.tigr.org/tdb/glimmerm/glmr_form.html




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