Web Service WSSignalP_3_1 SOAP Dk

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This service has been archived because it may not be active anymore (or is close to being non active). Please do not use it as it may not be accessible.

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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

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
Denmark Dk

Submitter/Source:
SeekDa (over 11 years ago)

Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/server.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/SignalP/SignalP_3_1.wsdl (download last cached WSDL file)

Documentation URL(s):
None
Description(s):
from provider's description doc (over 11 years ago)
	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 that
	            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.

	        * 'sequences' - 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: 'output' - prediction results:

	        For each input residue a record is output consisting of the
	        following fields:

	        'seqname'      sequence name
	        'source'       "signalp-3.1-nn" or "signalp-3.1-hmm" (fixed string)
	        'feature'      "signal" (fixed string)
	        'start','end'  predicted location of the signal peptide in the
	                       sequence (0-0 is no peptide is predicted)
	        'score'        prediction score:
	                       For "signalp-3.1-nn" D score, for "signalp-3.1-hmm"
	                       the signal peptide branch probability (see the
	                       article)
	        'strand'       N/A
	        'frame'        N/A
	        '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" for 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.
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