NetNGlyc 1.0a.ws0 Prediction of n-linked glycosylation sites in human proteins NOTE: a newer version of this service (NetNGlyc 1.0c.ws1) is available. WSDL NetNGlyc/NetNGlyc_1_0a_ws0.wsdl Schema definitions ws_netNglyc_1_0a_ws0.xsd ../common/ws_common_1_0b.xsd

Other versions and implementations

Examples of client side scripts using the service

Usage

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

perl netnglyc.pl < example.fsa 

Documentation

      INTRODUCTION

      This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation
      sites in human proteins using artificial neural networks that examine
      the sequence context of Asn-Xaa-Ser/Thr sequons. The method is described
      in detail in the following article:

      "Prediction of N-glycosylation sites in human proteins".
      R. Gupta, E. Jung and S. Brunak.
      In preparation, 2004.


      Alongside this Web Service the NetNGlyc method is also implemented as
      a traditional interactive WWW server at:

          http://www.cbs.dtu.dk/services/NetNGlyc

      The traditional server offers more detailed output (graphics), extended
      functionality and comprehensive documentation. It is suitable for close
      investigation of few proteins while this service is recommended for high
      throughput projects.

      NetNglyc 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?netNglyc

      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_0a.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 'netNglyc') 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 "N-glyc";
                 pos           - sequence residue;
                 score         - 'potential': N-glycosylation potential;
                 score         - 'jury': jury agreement (see below);
                 comment       - prediction result (see below).

                 The two scores above should be interpreted as follows:

                 Any potential crossing the default threshold of 0.5, represents
                 a predicted glycosylated site. The 'potential' score is the averaged
                 output of nine neural networks. For further information, the 'jury'
                 agreement column indicates how many of the nine networks support
                 the prediction. The final result is shown in the comment field; the
                 following values are possible:

                 for glycosylated sites:

                 +      potential>0.5
                 ++     potential>0.5 AND jury agreement (9/9)  OR potential>0.75
                 +++    potential>0.75 AND jury agreement
                 ++++   potential>0.90 AND jury agreement

                 and non-glycosylated sites:

                 -      potential<0.5
                 --     potential<0.5 AND jury agreement (all nine <0.5)
                 ---    potential<0.32 AND jury agreement

                 See http://www.cbs.dtu.dk/services/NetNGlyc/output.php for detailed
                 discussion of the prediction results. Please note that this Web
                 Service only predicts on asparagines in Asn-Pro-Ser/Thr sequons;
                 the interactive service mentioned above can be asked to predict on
                 all the asparagines in the input.


      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.