WSNetOGlyc_3_1d

By | September 22, 2011

INTRODUCTION

This Web Service implements NetOGlyc 3.1d. 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: An object of the type ‘sequencedata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
protein sequences with mandatory unique identifiers. Each
‘sequence’ is a pair of ‘id’ (identifier) and ‘seq’ (sequence
itself). The sequences must be written in 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: An object of the type ‘anndata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
the predition results. ‘annsource’ states the ‘method’ (in
this case always ‘netOglyc’) and ‘version’ (in this case 3.1b).
The objects of the type ‘annrecord’ hold the predictions for
a given residue in a given sequence, the fields are:

feature – always “O-glyc”;
pos – sequence residue;
score – G-score: general prediction score;
score – I-score: isolated site prediction score
(threonine residues only);
comment – appears only when the residue is predicted as
glycosylated, contains the letter ‘T’ or ‘S’.

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 NetPhos method should
go to Ramneek Gupta, ramneek@cbs.dtu.dk; technical questions concerning
the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Name
WSNetOGlyc_3_1d
Documentation
http://www.cbs.dtu.dk/services/NetOGlyc
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/simple.cgi
Topic
Biology
Type
Tags
, , , ,
Description

INTRODUCTION This Web Service implements NetOGlyc 3.1d. It predicts mucin type GalNAc O-glycosylation sites in mammalian proteins. The method is [...]

Further information

INTRODUCTION

This Web Service implements NetOGlyc 3.1d. 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: An object of the type ‘sequencedata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
protein sequences with mandatory unique identifiers. Each
‘sequence’ is a pair of ‘id’ (identifier) and ‘seq’ (sequence
itself). The sequences must be written in 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: An object of the type ‘anndata’ (see the complete definition
in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
the predition results. ‘annsource’ states the ‘method’ (in
this case always ‘netOglyc’) and ‘version’ (in this case 3.1b).
The objects of the type ‘annrecord’ hold the predictions for
a given residue in a given sequence, the fields are:

feature – always “O-glyc”;
pos – sequence residue;
score – G-score: general prediction score;
score – I-score: isolated site prediction score
(threonine residues only);
comment – appears only when the residue is predicted as
glycosylated, contains the letter ‘T’ or ‘S’.

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 NetPhos method should
go to Ramneek Gupta, ramneek@cbs.dtu.dk; technical questions concerning
the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or
Kristoffer Rapacki, rapacki@cbs.dtu.dk.

Original source
BioCatalogue

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