protein structure/function/analysis

Rob Kirkpatrick kirkpat at cc.?umanitoba?.ca
Mon Oct 27 12:54:36 EST 1997


In article <Deborah_Britt-2310971343430001 at cis-ts2-slip9.cis.brown.edu>,
Deborah_Britt at brown.edu (Deb Britt) wrote:

> I've got a clone (and more on the way), I've got the DNA sequence, now I'm
> faced with trying to make sense of it all.  Are there any good, general
> discussions in the literature about analyzing protein sequence?  For
> example: I can find open reading frames using computer analyzis, but how
> can I predict which is most likely the correct one (other than looking for
> a long stretch with no stops).  What characteristics define a leader
> sequence, or any of the various protein motifs?  Are there any references
> that can get me started on this kind of analysis, or do I just have to dig
> through literature and run blast searches until I notice sequence
> similarities?  If anyone can point me in the right direction to get
> started, I would appreciate the help.   Thanks!
> 
> Deb Britt
> 
> -- 
> Deborah Britt, Ph.D.
> Department of Medical Oncology
> Rhode Island Hospital

You can try out these sites on the web.  They are for finding promoter
regions, splice sites, protein motifs, etc.  The "art" of finding most of
this stuff is still a long ways from perfection, but these sites might
help you out a bit.

http://dot.imgen.bcm.tmc.edu:9331/gene-finder/gf.html
http://www.bionet.nsc.ru/TRRD/
http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html
http://www.public.iastate.edu/~pedro/pprotein_query.html
http://www.genome.ad.jp/SIT/MOTIF.html
http://ulrec3.unil.ch/software/COILS_form.html

Rob

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