NetOGlyc 3.1d.ws0Prediction of o-GalNAc (mucin type) glycosylation sites in mammalian proteins
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Documentation
INTRODUCTION
This Web Service implements NetOGlyc 3.1d.ws0. It predicts mucin type GalNAc
O-glycosylation sites in mammalian proteins. The method is described in
detail in the following article:
"Prediction, conservation analysis and structural characterization
of mammalian mucin-type O-glycosylation sites".
K. Julenius, A. Moelgaard, R. Gupta and S. Brunak.
Glycobiology, 15:153-164, 2005.
Alongside this Web Service the NetOGlyc method is also implemented as
a traditional paste-and-click WWW server at:
http://www.cbs.dtu.dk/services/NetOGlyc
The traditional server offers more detailed output (graphics), extended
functionality and comprehensive documentation. It is suitable for close
investigation of few proteins; this service is recommended for high
throughput projects.
NetOglyc is also available as a stand-alone software package to install
and run at the user's site, with the same functionality. For academic
users there is a download page at:
http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netOglyc
Other users are requested to write to software@cbs.dtu.dk for details.
WEB SERVICE OPERATION
This Web Service is fully asynchronous; the usage is split into the
following three operations:
1. runService
Input: The following parameters and data:
* 'signalp' run the signal peptide predictor 'signalp' on the
input sequences (no value, just presence/absence).
Information on the SignalP method can be found at:
http://www.cbs.dtu.dk/services/SignalP/
* 'sequencedata' mulitple elements of type 'sequence':
* 'sequence' answers to one sequence:
* 'id' unique identifier for the sequence;
* 'comment' optional comment;
* 'seq' protein sequence. The sequence must be written
using the one letter amino acid code:
`acdefghiklmnpqrstvwy' or `ACDEFGHIKLMNPQRSTVWY'.
Other letters will be converted to `X' and treated
as unknown amino acids. Other symbols,
such as whitespace and numbers, will be ignored.
Output: Unique job identifier
2. pollQueue
Input: Unique job identifier
Output: 'jobstatus' - the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
REJECTED, UNKNOWN JOBID or QUEUE DOWN
3. fetchResult
Input: Unique job identifier of a FINISHED job
Output: * 'annsource'
'method' name of the method, here always 'NetOGlyc';
'version' version of the method: here always '3.1d ws0';
'ann' annotations - one element per input sequence;
'sequence' standard sequence object;
'id' sequence identifier;
'annrecords/annrecord'
'feature' here always "O-glyc";
'pos' always present, indicates the position of the residue in the sequence;
'score'
'key'='G-score' G-score: general prediction score;
'value' G-score value;
'score'
'key'='I-score' I-score: isolated site prediction score (threonine residues only);
'value' I-score value;
'comment' appears only when the residue is predicted as glycosylated, contains
the letter 'T' or 'S'. It also contains 'signal peptide?' if a
residue in a predicted signal peptide is predicted as glycosylated.
A residue is predicted as glycosylated when the G-score for
that residue is >0.5. For threonines an additional score is
used: if the G-score is <0.5 but the I-score >0.5 and there
are no predicted neighbouring sites (distance <10 residues)
the residue is also predicted as glycosylated.
CONTACT
Questions concerning the scientific aspects of the NetOGlyc method should
go to Ramneek Gupta, ramneek@cbs.dtu.dk; technical questions concerning
the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.
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