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NetPhos 3.1b.ws1

Prediction of generic phosphorylation sites in eukaryotic proteins


WSDL NetPhos/NetPhos_3_1b_ws1.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_netphos_3_1_ws1.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/.

Other versions and implementations

Ver.Last updated
3.1b.ws1  2012-04-04(this version, most recent)
3.1b.ws0  2009-07-15

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
netphos.pl (5.0 KB) Perl 3.1b ws0 Edita Bartaseviciute
This script runs the NetPhos 3.1b.ws0 Web Service. It reads a FASTA file from STDIN and produces predictions in a simple table.
netphos_perl1 (5.6 KB) Perl 3.1b ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the NetPhos Web Service
netphos_python (4.9 KB) Python 3.1b ws1 Karunakar Bayyapu
Client script in Python (suds) running the NetPhos Web Service
test_netphos.pl (5.8 KB) Perl 3.1b ws0 Edita Bartaseviciute
This script runs the NetPhos 3.1b.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
netphos_soap_analysis (8.2 KB) 3.1b ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
example.fsa (1.3 KB)
check (6.1 MB)
netphos_php (4.6 KB) PHP 3.1b ws1 Karunakar Bayyapu
Client script in PHP running the NetPhos Web Service
netphos_csharp (5.5 KB) C# 3.1b ws1 Karunakar Bayyapu
Client script in C# (mono) running the NetPhos Web Service
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
netphos_perl2 (5.4 KB) Perl 3.1b ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the NetPhos Web Service
netphos_java (6.5 KB) Java 3.1b ws1 Karunakar Bayyapu
Client script in Java (apache) running the NetPhos Web Service

Documentation

    
    INTRODUCTION
    This Web Service implements NetPhos v. 3.1b.ws0. It predicts serine, threonine
    and tyrosine phosphorylation sites in eukaryotic proteins using ensembles
    of neural networks. Both generic and kinase specific predictions are
    performed. The method is described in detail in the following articles.

    Generic predictions:

    "Sequence and structure-based prediction of eukaryotic protein
    phosphorylation sites".
    Blom N, Gammeltoft S, Brunak S (1999). 
    J Mol Biol. 1999 Dec 17;294(5):1351-62.

    Kinase specific predictions:

    "Prediction of post-translational glycosylation and phosphorylation
    of proteins from the amino acid sequence".
    Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004).  
    Proteomics. 2004 4(6):1633-49. Review.

    Alongside this Web Service the NetPhos method is also implemented as
    two traditional paste-and-click WWW servers at:
        http://www.cbs.dtu.dk/services/NetPhos/  (generic predictions)
        http://www.cbs.dtu.dk/services/NetPhosK/ (kinase specific predictions)

    The traditional servers offer more detailed output (graphics), extended
    functionality  and comprehensive documentation. They are suitable for
    close investigation of few proteins; this service is recommended for high
    throughput projects.

    NetPhos 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?netphos

    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
         
            *  'ser'               Predict only on the S (serine) residues
                (no value, just presence/absence);
         OR
      *  'thr'               Predict  only on the T (threonine) residues
                              (no value, just presence/absence);
         OR
                                      
      *  'tyr'               Predict  only on the Y (tyrosine) residues
                             (no value, just presence/absence);
                                        
                                                                            
      *  'genericPred'       Run  generic predictions only, as in NetPhos 2.0
                              (no value, just presence/absence). 
            Information on the NetPhos-2.0 can be found at:
                        http://www.cbs.dtu.dk/services/NetPhos-2.0/
                                        
      *  'bestScore'         Report only the best (highest) score for each residue
                              (no value, just presence/absence);
                                        
      *  'kinaseSpec'        Run  kinase specific predictions only, as in NetPhosK 1.0
                             (no value, just presence/absence). 
            Information on the NetPhosK 1.0 can be found at: 
            http://www.cbs.dtu.dk/services/NetPhosK-1.0/
                                        
      *  'cutoff'            Report only the scores higher than cutoff. 
                             Choosing 0.5 implies reporting only the predicted sites.
        
                                        
      *  '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 'NetPhos';
                       'version'      version of the method: here always '3.1b ws0';

                       'ann'          annotations - one element per input sequence;
                         'sequence'     standard sequence object;
                         'id'          sequence identifier;
                       'annrecords/annrecord'
                         'feature'     active kinase ('unsp' for generic predictions);
                         'pos'         always present, indicates the position of the residue in the sequence; 
                         'score'
                           'key'       score key name, here always 'main', indicating the main prediction score;
                           'value'     prediction score value, if higher than 0.5 the residue
                     is a predicted phosphorylation site, the higher
                     the score the more secure the prediction;
                         'comment'     appears only when the score is higher than 0.5, contains the word 'YES'.
         
         
    CONTACT

    Questions concerning the scientific aspects of the NetPhos method should
    go to Thomas Sicheritz, thomas@cbs.dtu.dk; technical questions concerning
    the Web Service should go to Karunakar Bayyapu, karun@cbs.dtu.dk or
    Kristoffer Rapacki, rapacki@cbs.dtu.dk.