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NetNES 1.1.ws0

Template service


WSDL NetNES/NetNES_1_1_ws0.wsdl
Schema definitions http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd
http://www.cbs.dtu.dk/ws/NetNES/ws_netnes_1_1_ws0.xsd
http://bioxsd.org/BioXSD-0.4.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
netnes.pl (3.8 KB) Perl 1.1 ws0 Edita Bartaseviciute
This script runs the NetNES 1.1.ws0 Web Service. It reads FASTA file from STDIN and produces predictions in a simple table.
example.fsa (1.3 KB)
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
test_netnes.pl (5.1 KB) Perl 1.1 ws0 Edita Bartaseviciute
This script runs the NetNES 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/NetNES/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/NetNES/examples/netnes.pl

perl netnes.pl < example.fsa 

Documentation

      INTRODUCTION

      This Web Service implements NetNES v. 1.1.ws0. It predicts leucine-rich nuclear export signals (NES) 
      in eukaryotic proteins using a combination of neural networks and hidden Markov models. 
      The method is described in detail in the following article:
      
      Analysis and prediction of leucine-rich nuclear export signals
      Tanja la Cour, Lars Kiemer, Anne Molgaard, Ramneek Gupta, Karen Skriver and Soren Brunak
      Protein Eng. Des. Sel., 17(6):527-36, 2004. 
      
      Alongside this Web Service the NetNES method is also implemented as
      a traditional paste-and-click WWW server at:
      
            http://www.cbs.dtu.dk/services/NetNES/
      
      The traditional server offers extended functionality and comprehensive 
      documentation. It is suitable for close investigation of few proteins; 
      this service is recommended for high throughput projects.


      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
                 
                 *  'sequenceRecord'          answers to one sequence:
                      * 'sequence'              protein sequence. The sequence must be written 
                                                using the one letter amino acid code in capital letters:
                                                `ACDEFGHIKLMNPQRSTVWY'.Other letters will be converted 
                                                to `X' and treated as unknown amino acids. Other symbols, 
                                                such as whitespace and numbers, will be ignored;
                      * 'customNote'            optional comment;
                      * 'formalReference' 
                          * 'accession'           unique identifier for the sequence.
         
         
         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: *  'annotatedSequence'          annotations - one element per input sequence;
                      *  'sequenceRecord'          answers to one sequence:
                          *  'sequence'              protein sequence given as an input;
                          *  'formalReference'
                              * 'accession'            unique identifier for the input sequence;
                                  
                      * 'annotation'
                          *  'feature'
                              *  'name'                feature name, here always 'NetNES';
                          *  'occurence'             occurence of a feature in a sequence;
                              *  'position'            always present, indicates the position of each residue;
                                  *  'point'             residues number;
                              *  'evidence'
                                  *  'predicted'
                                      *  'methodId'        id composed of today's day, name and version of the method.
                                                           Example: 6-4-2010NetNES-1.1ws0;
                                      *  'score'
                                          *  'type' = 'ANN'  Artificial Neural Network (ANN) score type;
                                          *  'value'         ANN prediction score value; 
                                                                                
                                          *  'type' = 'HMM'  Hidden Markov Model (HMM) score type;
                                          *  'value'         HMM prediction score value;
                                           
                                          *  'type' = 'NES'  NES score type - the main prediction score, calculated from ANN and HMM scores;
                                          *  'value'         NES prediction score value;                                                             
                                                                   
                                      *  'verdict'         contains 'Present' if the NES score exceeds the threshold, indicating that particular residue is 
                                                           expected to participate in a nuclear export signal. Otherwise contains 'Impossible'.
      
      
      Please note, that input and output data types of the NetNES v. 1.1.ws0 Web Service 
      are defined by the external canonical XML-Schema - BioXSD.
      
      CONTACT

      Technical questions concerning the Web Service 
      should go to Edita Bartaseviciute,edita@cbs.dtu.dk 
      or Kristoffer Rapacki, rapacki@cbs.dtu.dk.