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

NetChop 3.1.ws1

Prediction of proteasomal cleavages (MHC ligands)

WSDL NetChop/NetChop_3_1_ws1.wsdl
Schema definitions ../common/ws_common_1_0b.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

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription (5.4 KB) Perl 3.1 ws0 Edita Bartaseviciute
This script runs the NetChop 3.1.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
netchop_java (6.5 KB) Java 3.1 ws1 Karunakar Bayyapu
Client script in Java (apache) running the NetChop Web Service
netchop_perl2 (5.4 KB) Perl 3.1 ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the NetChop Web Service
netchop_php (4.5 KB) PHP 3.1 ws1 Karunakar Bayyapu
Client script in PHP running the NetChop Web Service
netchop_csharp (5.5 KB) C# 3.1 ws1 Karunakar Bayyapu
Client script in C# (mono) running the NetChop Web Service (4.8 KB) Perl 3.1 ws0 Edita Bartaseviciute
This script runs the NetChop 3.1.ws0 Web Service. It reads a FASTA file from STDIN and produces predictions.
netchop_perl1 (5.6 KB) Perl 3.1 ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the NetChop Web Service
example.fsa (1.3 KB)
netchop_soap_analysis (8.3 KB) 3.1 ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
netchop_python (4.9 KB) Python 3.1 ws1 Karunakar Bayyapu
Client script in Python (suds) running the NetChop Web Service (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)



    This Web Service implements NetChop v. 3.1.ws0. It produces neural network
    predictions for cleavage sites of the human proteasome. The method is
    described in detail in the following article:

    The role of the proteasome in generating cytotoxic T cell epitopes:
    Insights obtained from improved predictions of proteasomal cleavage.
    M Nielsen, C Lundegaard, O Lund, and C Kesmir.
    Immunogenetics., 57(1-2):33-41, 2005.

    Alongside this Web Service the NetChop method is also implemented as
    a traditional click-and-paste WWW server at:
    NetChop 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:

    Other users are requested to write to for details.


    This Web Service is fully asynchronous; the usage is split into the
    following three operations:

    1. runService    

    Input:  The following parameters and data:

            *  'method'              prediction method:
                                        0 for "C term 3.0", 1 for "20S 3.0";

            *  'threshold'           threshold for yes/no decision.
                                     The default is 0.5; increasing the threshold results in better
                                     specificity, but worse sensitivity;

            *  '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,

    3. fetchResult
    Input:  Unique job identifier of a finished job

    Output: * 'annsource'
                'method'              name of the method, here always 'NetChop';
                'version'             version of the method: here always '3.1 ws0';

              'ann'                 annotations - one element per input sequence;
                'sequence'            standard sequence object;
                  'id'                  sequence identifier;
                  'feature'             feature name, here always 'NetChop';
                  'pos'                 always present, indicates the position in the sequence;
                    'key'                 score key name, here always 'main', indicating the main prediction score;
                    'value'               prediction score value;
                  'comment'             gives 'S' for identified cleavage sites. Appears only if the prediction score 
                                        is greater than the threshold.


    Questions concerning the scientific aspects of the NetChop method should go
    to Morten Nielsen,; technical question concerning the Web
    Service should go to Karunakar Bayyapu, or Kristoffer