[Fwd: Rice 14-3-3]

[Pankaj Jaiswal]

"Ferl, Robert J." wrote:
> 
> Dear Pankaj,
> 
> Thank you for your note. Give us some time to look things over and we will
> see if we have any suggestions for you. I agree that good curation of
> nomenclature is important at the very least. But the understanding of the
> evolutionary paths is even more important. So give us a couple of days to
> look at your alignments and compare them to ours (we keep an alignment of
> all the 14-3-3s in the databases). Also, I should mention even before I look
> at your data that alignments can vary (especially in noise) depending upon
> which areas of the proteins are included or excluded from the alignment.
> 
> Take care, talk to you later,
> Rob
> 
> -----Original Message-----
> From: Pankaj Jaiswal [mailto:pj37 at cornell.edu]
> Sent: Friday, July 05, 2002 12:05 PM
> To: robferl at ufl.edu
> Subject: Rice 14-3-3
> 
> Dear Rob,
> 
> I was going through your excellent review article that just appeared in
> Genome
> Biology 3(7) and tried to classify the 14-3-3 family of proteins from rice.
> I am
> having some difficulty as you would see in the attached powerpoint file
> (rice_14-3-3_tree.ppt), showing the phylogenetic tree drawn from the clustal
> alignment of Arabidopsis and rice proteins . The non-epsilons from
> Arabidopsis
> (G14kappa, lambda, chi omega and phi) referred in your review appear to be
> with
> the epsilons (epsilon, omicron, mu and iota). Even if I take the Arabidopsis
> proteins the situation does not change. I don't know if the situation will
> change if I take all the sequences from other organisms, referred in your
> review, I haven't given it a try. Anyhow, the problem is how should I
> classify
> the rice 14-3-3 proteins as I am doing the curation of the rice protein
> database
> at Gramene
> 
> http://www.gramene.org/perl/protein_search
> 
> specific URL for members of 14-3-3 family
> http://www.gramene.org/perl/protein_advanced?pfam=PF00244
> 
> Also there is inconsistency of nomenclature in rice 14-3-3. I would like to
> get
> it fixed and it will be great if you could help me in curation of the
> 14-3-3s
> from rice.
> 
> Looking forward to your suggestions.
> 
> Best regards
> 
> Pankaj
> 
> ******************************************
> Pankaj Jaiswal, Ph.D.
> Postdoctoral Associate
> Dept. of Plant Breeding
> Cornell University
> Ithaca, NY-14853, USA
> 
> Tel:+1-607-255-3103 / Fax:+1-607-255-6683
> E mail: pj37 at cornell.edu
> http://www.gramene.org
> ******************************************

-- 

******************************************
Pankaj Jaiswal, Ph.D.                                   
Postdoctoral Associate
Dept. of Plant Breeding                             
Cornell University                                   
Ithaca, NY-14853, USA   

Tel:+1-607-255-3103 / Fax:+1-607-255-6683
E mail: pj37 at cornell.edu
http://www.gramene.org   
******************************************