Locating exons

Keith Robison robison at lipid.harvard.edu
Tue Jul 26 23:08:55 EST 1994

Chad Price x7936 (cprice at unmc.edu) wrote:
: Ronald N. Cole (cole at NJORD.SCS.UIUC.EDU) wrote:
: : Hello,
: :         We are studying exons.  We are looking for a piece of software, or a
: : database which will help us.

: : Ideally we would like to have a program where;

: : 1.) We provide a specific pdb filename (eg. pdb1mbo.ent)
: : 2.) We recieve a complete DNA sequence file containing the location of exons

If you are looking for exons in human DNA, then try GRAIL.
It's available via E-mail to grail at ornl.gov.

GeneFinder is the exon hunter used in the C.elegans project;
contact one of the C.elegans groups (Wash U. @ St.Louis)
for it.

As another poster put it, this is a bit of an unsolved problem
in the general case -- current approaches are based on organism-specific
tables which need lots of good examples to learn on.

Also, in case you haven't already, BLASTX is very good at  finding
exons, if those exons happen to be homologous to known proteins
(and BLASTN is even better, as long as someone has sequenced
the cDNA for you :-)

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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