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ProtFun 2.2.ws0

Protein functional category and enzyme class (Eukarya)


WSDL ProtFun/ProtFun_2_2_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_protfun_2_2_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
protfun.pl (2.1 KB) Perl 2.2 ws0 Peter Fischer Hallin
This is a ProtFun ws client script. It reads a protein fasta file from STDIN and produces an annotation output
example.fsa (278 B)
xml-compile.pl (3.2 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)

Usage

# download the required scripts
wget http://www.cbs.dtu.dk/ws/ProtFun/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/ProtFun/examples/example.fsa
wget http://www.cbs.dtu.dk/ws/ProtFun/examples/protfun.pl

perl protfun.pl < example.fsa 

Documentation

      The ProtFun 2.2 server produces  ab initio  predictions of protein function from sequence. 
      The method queries a large number of other feature prediction servers to obtain information
      on various post-translational and localization

      The service runs asynchronously, with three operations "runServcie", "pollQueue", and "fetchResult"

      The service is also available as a web application, http://www.cbs.dtu.dk/services/ProtFun

      1. runService    

    Input:  The following parameters and data:

            * 'sequencedata'   [containing mulitple 'sequence' element]
              * 'sequence'
                * 'id'         Unique identifier for the sequence
                * 'comment'    Optional comment
                * 'seq'        protein sequences, with unique identifiers (mandatory) 
                               The sequences 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

    For further documentation on the predicted features, please read http://www.cbs.dtu.dk/services/ProtFun/output.php
    Output: 
            * 'annsource'
                'method'      : Name of the method
                'version'     : Version of the methods

            * 'ann'             (array of annotations - one element per input sequence)
                'sequence'      (standard sequence object)
                 'id'        : Sequence identifier
                 'comment'   : Sequence comment
                 'seq'       : Sequence
               'annrecords'    (array of predicted features for this sequence)
                 'annrecord'   (annotation record)
                  'feature    : Category:class (e.g. "Functional category:Transport_and_binding"
                  'global'    : "global", global feature prediciton
                  'score'
                    'key'     : "prob", Estimated probability that the entry belongs to the class in question
                    'value    : The score value
                  'score'
                    'key'     : "odds", Odds that the sequence belongs to that class/category. It is independent of the probability
                    'value    : The score value
                  'score'
                    'key'     : "flag" The score with the highest information content is marked '1'  
                                (unless the odds score is lower than 1)
                    'value    : 1/0