NetOglyc ( was: removing o-glycosylation)

[allan hey]

In article 
<Pine.A32.3.91.950903071318.18610B-100000 at freenet3.freenet.ufl.edu>, 
afn26055 at freenet.ufl.edu says...
>
>Alan,
>You mentioned a NetOglyc prediction service. Could you follow up with 
>info for accessing this service. Thank you.
>Ed
>FERMCO

NetOglyc is a free service for prediction of O-glycosylation, provided 
by the Center for Biological Sequence Analysis at The Technical 
University of Denmark in Lyngby, Denmark.  I've taken the liberty of 
copying the following from them:

*************** NetOglyc Mail Server V1.0 *************** 
		      
Prediction of O-glycosylation of mammalian proteins

Center for Biological Sequence Analysis
The Technical University of Denmark
DK-2800 Lyngby, Denmark  



DESCRIPTION:

The  NetOglyc  mail  server  is  a  service  producing  neural  network
predictions of mucin type O-glycosylation sites  in  mammalian proteins 
as described in: J.E. Hansen, O. Lund,  J. Engelbrecht,  H. Bohr,  J.O. 
Nielsen, J.E.S. Hansen and S. Brunak, Prediction of O-glycosylation  of
mammalian proteins: Specificity  patterns   of   UDP-GalNAc:polypeptide
N-acetylgalactosaminyltransferase.  The   Biochemical   Journal,   308, 
801-813, 1995. 

ABSTRACT:

The specificity of the enzyme(s) catalyzing the covalent  link  between
the hydroxyl side-chains of serine or threonine and  the  sugar  moiety
GalNAc is unknown. Pattern recognition by  artificial  neural  networks
and weight matrix algorithms  was  performed  to  determine  the  exact
position of in vivo O-linked GalNAc glycosylated serine  and  threonine
residues from the primary sequence exclusively. The  acceptor  sequence
context for O-glycosylation of serine was found to differ from that  of
threonine and the two types  were  therefore  treated  separately.  The
context of the sites showed a high abundance  of  proline,  serine  and
threonine extending far beyond the previously reported region  covering
positions -4 through +4  relative  to  the  glycosylated  residue.  The
O-glycosylation sites  were  found  to  cluster  and  to  have  a  high
abundance in the amino-terminal part of the  protein.  The  sites  were
also found to have an increased preference for three different  classes
of beta-turns. No simple consensus like rule could be deduced  for  the
complex glycosylation sequence acceptor patterns. The  neural  networks
were trained on the hitherto largest data  material  consisting  of  48
carefully   examined    mammalian    glycoproteins    comprising    264
O-glycosylation sites. For detection  neural  network  algorithms  were
much more reliable than weight matrices. The networks  correctly  found
60-95% of the O-glycosylated serine/threonine residues  and  89-97%  of
the non-glycosylated residues in two independent  test  sets  of  known
glycoproteins.  A  computer  server  using  E-mail  for  prediction  of
O-glycosylation sites has been implemented and made publicly available. 


CURRENT NETWORK

The network will be updated and predictions can alter due to  different 
versions. The network is balanced  to  give optimal predictions whether 
you submit sequences  with  no  homology  to  the  known O-glycosylated 
proteins or not. If however the submitted sequence is  very close to or 
identical to the sequences  in  our training dataset, wewill notify you 
by sending you  both the assigment  of  the  homologous  (or identical) 
sequence in our data set and the prediction. 


FURTHER INFORMATION:

The NetOglyc server returns a help file if the submitted file  contains
the word `help'. 
	
CONFIDENTIALITY

Your submitted sequences  will  be  deleted  automatically  immediately
after processing by NetOglyc.

*******************
The procedure is to send an E-mail to netOglyc at genome.cbs.dtu.dk.  The 
first line should be a greater-then sign (>) followed by the name for 
the sequence.  On the next line put the sequence (in single letter 
code), followed by an empty line to indicate the end of the sequence.  
Several sequences can be submitted in the same e-mail.  You get the 
results back by e-mail - in my experience within a few hours of 
submitting the sequence.  

Hope this is of help to you!

Allan