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NetMHCcons 1.0.ws1

Prediction of binding of peptides to any known MHC class I molecule


WSDL NetMHCcons/NetMHCcons_1_0_ws1.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_netmhccons_1_0_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/.

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
netmhccons.pl (6.8 KB) Perl 1.0 ws0 Edita Karosiene
This script runs the NetMHCcons 1.0.ws0 Web Service. It reads a FASTA file from STDIN and produces predictions.
netmhccons_perl2 (5.5 KB) Perl 1.0 ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the NetMHCcons Web Service
netmhccons_csharp (5.5 KB) C# 1.0 ws1 Karunakar Bayyapu
Client script in C# (mono) running the NetMHCcons Web Service
netmhccons_perl1 (5.6 KB) Perl 1.0 ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the NetMHCcons Web Service
netmhccons_python (4.9 KB) Python 1.0 ws1 Karunakar Bayyapu
Client script in Python (suds) running the NetMHCcons Web Service
netmhccons_soap_analysis (8.3 KB) 1.0 ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
example.fsa (1.3 KB)
netmhccons_php (4.6 KB) PHP 1.0 ws1 Karunakar Bayyapu
Client script in PHP running the NetMHCcons Web Service
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
netmhccons_java (6.5 KB) Java 1.0 ws1 Karunakar Bayyapu
Client script in Java (apache) running the NetMHCcons Web Service

Documentation

    
    This Web Service implements NetMHCcons v. 1.0.ws0. It predicts binding
    of peptides to any known MHC class I molecule. This is a consensus method for 
    MHC class I predictions integrating three state-of-the-art methods NetMHC, 
    NetMHCpan and PickPocket to give the most accurate predictions.

      http://www.cbs.dtu.dk/services/NetMHCcons/abstract.php


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

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

        
    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:

            *  'allele'           MHC class I allele which you want to get the predictions for.
                See the list of available alleles:
                http://www.cbs.dtu.dk/services/NetMHCcons/MHC_allele_names.txt
      
      *  'sort'             Output sorting by descending predicted binding affinity (just present or absent);

            *  'length'           Peptide length between 8 and 11 amino acids. Several lengths are 
                possible and should be specified separated by comas (i.e.'8,9');
              
            *  'method'           Method which you want to use for predictions. Possible values are 'NetMHC', 'NetMHCpan'
                'PickPocket' and 'NetMHCcons' (which is the default method).Note that using NetMHC method, 
                the list of possible alleles becomes shorter:
                http://www.cbs.dtu.dk/services/NetMHCcons/MHC_allele_names_NetMHC.txt
                                     
                *  'rankS'            Threshold for Strong binding peptides expressed as %Rank; 

                *  'rankW'            Threshold for Weak binding peptides expressed ad %Rank;
        
            *  'affS'             Threshold for Strong binding peptides expressed as IC50 value;
      *  'affS'             Threshold for Weak binding peptides expressed as IC50 value;
      
              
            *  '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 'NetMHCcons';
                  'version'             version of the method: here always '1.0 ws0';

                'ann'                 annotations - one element per input sequence;
                  'sequence'            standard sequence object;
                    'id'                  sequence identifier;
                  'annrecords/annrecord'
                    'feature'             allele name;
              'range'               always present, indicates the range in the sequence: 
                      'begin'               begin position of the peptide;
                          'end'                 end position of the peptide;
              'score'
          'key'='log_score'     prediction score; 
          'value'               score value for 'log_score'. The value is given 
              as 1 - log50k(aff), where log50k is the 
              logaritm with base 50.000, and aff is the 
              affinity in nM units;
                        'score'
          'key'='aff'      predicted binding affinity;
          'value'               score value for 'aff'. The predicted 
              binding affinity as IC50 value in nM;
                        'score'
          'key'='rank'          %Rank;
          'value'               score value for 'rank'. % Rank of prediction score 
                                  to a set of 200.000 random natural 9mer peptides
                  'comment'              gives 'SB' for identified strong binders and 'WB' 
                          for identified weak binders. The peptide will be 
                                          identified as a strong binder if the % Rank OR 
                                          binding affinity (IC50) is below the specified 
                                          threshold for the strong binders. The peptide will 
                                          be identified as a weak binder if the % Rank OR 
                                          binding affinity (IC50) is above the threshold 
                                          of the strong binders but below the specified 
                                          threshold for the weak binders
                                            
    
    More comprehensive information about the output could be found at:
           http://www.cbs.dtu.dk/services/NetMHCcons/output.php
 
    CONTACT

    Questions concerning the scientific aspects of the NetMHCcons method should go
    to Morten Nielsen, mniel@cbs.dtu.dk or Edita Karosiene edita@cbs.dtu.dk.
        Technical question concerning the Web Service should go to 
        Karunakar Bayyapu, karun@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.