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SignalP 3.1.ws0

Prediction of signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences


WSDL SignalP/SignalP_3_1_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_signalp_3_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
soapui-settings.xml (869 B) XML
test_signalp.pl (3.4 KB) Perl 3.1 ws0 Peter Fischer Hallin
Runs SignalP Web Service.
signalp.pl (2.0 KB) Perl 3.1 ws0 Peter Fischer Hallin
Runs SignalP on one or more sequences, read in fasta format from STDIN
example.fsa (1.3 KB)
xml-compile.pl (3.2 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
soapui.log (4.9 KB)
soapui-errors.log (0 B)

Usage

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

perl signalp.pl < example.fsa 

Documentation

    INTRODUCTION

    This Web Service implements SignalP v. 3.1. It predicts  the presence and
    location of signal peptide cleavage sites in amino acid sequences from
    different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes,
    and eukaryotes. The method incorporates a prediction of cleavage sites
    and a signal peptide/non-signal peptide prediction based on a combination
    of several artificial neural networks and hidden Markov models. The method
    is described in detail in the following article:

    Improved prediction of signal peptides: SignalP 3.0.
    J D Bendtsen, H Nielsen, G v Heijne and S Brunak.
    J. Mol. Biol., 340:783-795, 2004.

    The difference between v. 3.0 and this version is only technical; the
    predictions are the same.

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

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

    The traditional server offers more detailed output (graphics), extended
    functionality  and comprehensive documentation. It is suitable for close
    investigation of few proteins; this service is recommended for high
    throughput projects.

    SignalP 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?signalp

    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)
                "euk"     eukaryotes
                "gram-"   Gram-negative prokaryotes
                "gram+"   Gram-positive prokaryotes

            * 'method' - prediction method (optional)
                "nn"      neural network only
                "hmm"     hidden Markov models only
                "nn+hmm"  both methods (default)

            * 'thnn' - threshold for yes/no decision by neural nets (optional)
                The threshhold setting affects the 'comment' field in the
                output (see below): if the neural net score is higher than
                the selected threshold the comment will be "Y", else "N".
                The default thresholds are 0.43 for "euk", 0.45 for "gram+"
                and 0.44 for "gram-"; the defaults have been shown to give
                the highest correlation coefficient on test data.
                Note: 'thnn' does not affect the signalp-hmm prediction output.

            * 'sequencedata'   [containing multiple '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. All the input sequences are truncated to 70 aa from
                               the N-terminal. Currently, at most 2,000 sequences are allowed
                               per submission.

    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'      : SignalP (options ...)
                'version'     : 3.1 ws0

            * '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    : either 'signal-nn' or 'signal-hmm'
                 'range'
                   'begin'   : 1
                   'end'     : End postion of signal
                 'score'
                   'key'     : Either nn_score or hmm_score
                   'value    : Prediction score:
                                For "signalp-3.1-nn" D score, for "signalp-3.1-hmm"
                                the signal peptide branch probability (see the
                                article)
                 'comment     : Answer: For "signalp-3.1-nn" the answer is "Y" (yes) and "N"
                                (no) depending on the selected threshold. 
                               For "signalp-3.1-hmm" the answer is "S" f or signal
                               peptide, "A" for signal anchor ("euk" only) and "Q"
                               for none of the above.

    KNOWN BUGS

    2007-01-30    Error handling: some error messages may be non-informative;
                  fix in progress;

    2007-01-29    The server side may time out processing large submission;
                  temporary fix: submit not more than 2,000 sequences at a
                  time; permanent fix in progress.


    CONTACT

    Questions concerning the scientific aspects of the SignalP method should
    go to Henrik Nielsen, hnielsen@cbs.dtu.dk; technical questions concerning
    the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or
    Kristoffer Rapacki, rapacki@cbs.dtu.dk.