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TargetP 1.1.ws0

Template service


WSDL TargetP/TargetP_1_1_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_targetp_1_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
example.fsa (1.3 KB)
targetp.pl (4.4 KB) Perl 1.1 ws0 Edita Bartaseviciute
This script runs the TargetP 1.1 ws0 Web Service. It reads FASTA from STDIN and produces predictions in a simple tables.
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
test_targetp.pl (4.8 KB) Perl 1.1 ws0 Edita Bartaseviciute
This script runs the TargetP 1.1 ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.

Usage

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

perl targetp.pl -P|-N [-t float] < example.fsa 

Documentation

    INTRODUCTION
          
    This Web Service implements TargetP v.1.1.ws0. It predicts the 
    subcellular location of eukaryotic protein sequences. The assignment 
    is based on the predicted presence of any of the N-terminal presequences:
    chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) 
    or secretory pathway signal peptide (SP). The method is described in 
    detail in the following article:
          
    Locating proteins in the cell using TargetP, SignalP, and related tools.
    Olof Emanuelsson, Soren Brunak, Gunnar von Heijne, Henrik Nielsen
    Nature Protocols 2, 953-971 (2007).
          
    Alongside this Web Service the TargetP method is also implemented as
    a traditional click-and-paste WWW server at:
          
      http://www.cbs.dtu.dk/services/TargetP/ 
          
    TargetP 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?targetp
            
    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
             
            *  'organism'                Organism type of the input sequences (mandatory):
                                           "P"    plant;
                                           "N"    non-plant. 
                                                                                                     
            *  'cleavage'                Include cleavage site prediction.
                                         (no value, just presence/absence); 
                                                                                      
            *  'cTP'                     A cutoff for predicting cTP. 
                                         The value must be between 0.0 and 1.0.
                                                
            *  'SP'                      A cutoff for predicting SP. 
                                         The value must be between 0.0 and 1.0.
                                                
            *  'mTP'                     A cutoff for predicting mTP. 
                                         The value must be between 0.0 and 1.0.
                                                
            *  'other'                   A cutoff for predicting "other". 
                                         The value must be between 0.0 and 1.0.

            *  '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 'TargetP';
                  'version'                 version of the method: here always '1.1 ws0';

                'ann'                       annotations - one element per input sequence;
                  'sequence'                  standard sequence object;
                    'id'                        sequence identifier;
                  'annrecords/annrecord'
                    'feature'                   feature name, here always 'TargetP';
                    'global'                    always present, indicates the whole sequence;                               
                             
                    'score'
                      'key'='cTP'                 prediction for chloroplast transit peptide;
                      'value'                     NN prediction score for "cTP";
                                                  This score is present only for the plants.
                    'score'
                      'key'='mTP'                 prediction for mitochondrial targeting peptide; 
                      'value'                     NN prediction score for "mTP";
                             
                    'score'
                      'key'='SP'                  prediction for secretory pathway signal peptide; 
                      'value'                     NN prediction score for "SP";                               
                             
                    'score'
                      'key'='other'               prediction for other location of the protein; 
                      'value'                     NN prediction score for "other";
                               
                    'score'
                      'key'='RC'                 reliability class of prediction; 
                      'value'                    the value fo "RC". RC is a measure of the size of 
                                                 the difference ('diff') between the highest (winning) 
                                                 and the second highest output scores. There are 
                                                 5 reliability classes, the lower the value of RC 
                                                 the safer the prediction;
                            
                    'comment'                  Contains answer of prediction of localization, based 
                                               on the scores above. The possible values are:
                                                 "C" - Chloroplast, i.e. the sequence contains cTP, 
                                                       a chloroplast transit peptide;
                                                 "M" - Mitochondrion, i.e. the sequence contains mTP, 
                                                       a mitochondrial targeting peptide;
                                                 "S" - Secretory pathway, i.e. the sequence contains SP,
                                                       a signal peptide;
                                                 "_" - Any other location;
                                                 "*" - "don't know"; indicates that cutoff restrictions 
                                                       were set and the winning network output score was 
                                                       below the requested cutoff for that category. 
                                                It also contains predicted presequence length if TargetP
                                                was asked to perform cleavage site predictions.
             
             
    More comprehensive information about the output could be found at:
             
       http://www.cbs.dtu.dk/services/TargetP/output.php
             
             
    CONTACT

    Questions concerning the scientific aspects of the NetCTL method should 
    go to Olof Emanuelsson, olof@sbc.su.se; technical question concerning 
    the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or 
    Kristoffer Rapacki, rapacki@cbs.dtu.dk.