Web Service WSSignalP_3_0 SOAP Dk

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Annotations: 12 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 7 Total number of annotations sourced from other registries. 4


Center for Biological Sequence Analysis (CBS)

Denmark Dk

SeekDa (over 11 years ago)

Base URL:

WSDL Location:
http://pigdb.org/ws/SignalP/SignalP_3_0.wsdl (download last cached WSDL file)

Documentation URL(s):
from provider's description doc (over 11 years ago)

This Web Service implements SignalP v. 3.0. 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.

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


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; write to
software@cbs.dtu.dk for details.


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

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

        * 'sequences' - protein sequences, with unique identifiers 
          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.
          At most 2,000 sequences and 200,000 amino acids per submission;
          each sequence not more than 6,000 amino acids.

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,

3. fetchResult

Input:	Unique job identifier of a finished job

Output: 'output' - prediction results
        For each input residue a record is output consisting of the
        following fields:

        seqname        sequence name
        source         "signalp-3.0-nn" or "signalp-3.0-hmm" (fixed string)
        feature        "signal" (fixed string)
        start,end      predicted position of the signal peptide in the
                       sequence (0-0 is no peptide is predicted)
        score          prediction score (D score, see the article)
        strand,frame   N/A
        comment        answer ("Y" or "S" for yes, "n" or "Q" for no)


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