Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

NetOGlyc 3.1d.ws0

Prediction of o-GalNAc (mucin type) glycosylation sites in mammalian proteins


WSDL NetOGlyc/NetOGlyc_3_1d_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_netoglyc_3_1_ws0.xsd

We recommend that the first time users should load the WSDL file above to SoapUI and investigate the Web Service operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP. It can be downloaded free of charge from http://www.soapui.org/.

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
netoglyc_php (4.6 KB) PHP 3.1d ws1 Karunakar Bayyapu
Client script in PHP running the NetOGlyc Web Service
netoglyc_perl2 (5.4 KB) Perl 3.1d ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the NetOGlyc Web Service
netoglyc_python (4.9 KB) Python 3.1d ws1 Karunakar Bayyapu
Client script in Python (suds) running the NetOGlyc Web Service
test_netoglyc.pl (4.7 KB) Perl 3.1 ws0 Edita Bartaseviciute
This script runs the NetOGlyc 3.1d.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
netoglyc_csharp (5.6 KB) C# 3.1d ws1 Karunakar Bayyapu
Client script in C# (mono) running the NetOGlyc Web Service
example.fsa (1.3 KB)
netoglyc_soap_analysis (8.3 KB) 3.1d ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
netoglyc.pl (3.9 KB) Perl 3.1 ws0 Edita Bartaseviciute
This script runs the NetOGlyc 3.1d.ws0 Web Service. It reads a FASTA file from STDIN and produces predictions in a simple table.
netoglyc_java (6.5 KB) Java 3.1d ws1 Karunakar Bayyapu
Client script in Java (apache) running the NetOGlyc Web Service
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
netoglyc_perl1 (5.6 KB) Perl 3.1d ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the NetOGlyc Web Service

Usage

# download the required scripts
wget http://www.cbs.dtu.dk/ws/NetOGlyc/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/NetOGlyc/examples/netoglyc.pl

perl netoglyc.pl [-sp] < example.fsa 

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.