Web Service NetNGlyc - Prediction of n-linked glycosylation sites in human proteins SOAP

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This service has been archived because it may not be active anymore (or is close to being non active).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

Specified Name (from WSDL): WSNetNGlyc_1_0a_ws0 |
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Annotations: 17 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 13 Total number of annotations sourced from other registries. 3

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
European Union

Submitter/Source:
rapacki (over 11 years ago)

Base URL:
http://ws.cbs.dtu.dk/cgi-bin/soap/ws/quasi-1.2.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/NetNGlyc/NetNGlyc_1_0a_ws0.wsdl (download last cached WSDL file)

Description(s):
from provider's description doc (over 11 years ago)
		INTRODUCTION

		This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation
		sites in human proteins using artificial neural networks that examine
		the sequence context of Asn-Xaa-Ser/Thr sequons. The method is described
		in detail in the following article:

		"Prediction of N-glycosylation sites in human proteins".
		R. Gupta, E. Jung and S. Brunak.
		In preparation, 2004.


		Alongside this Web Service the NetNGlyc method is also implemented as
		a traditional interactive WWW server at:

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

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

		NetNglyc 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?netNglyc

		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:  An object of the type 'sequencedata' (see the complete definition
		           in http://www.cbs.dtu.dk/ws/common/ws_common_1_0a.xsd) holding
		           protein sequences with mandatory unique identifiers. Each
		           'sequence' is a pair of 'id' (identifier) and 'seq' (sequence
		           itself). The sequences must be written in 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

		   Output: An object of the type 'anndata' (see the complete definition
		           in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding
		           the predition results. 'annsource' states the 'method' (in
		           this case always 'netNglyc') and 'version' (in this case 3.1b).
		           The objects of the type 'annrecord' hold the predictions for
		           a given residue in a given sequence, the fields are:

		           feature       - always "N-glyc";
		           pos           - sequence residue;
		           score         - 'potential': N-glycosylation potential;
		           score         - 'jury': jury agreement (see below);
		           comment       - prediction result (see below).

		           The two scores above should be interpreted as follows:

		           Any potential crossing the default threshold of 0.5, represents
		           a predicted glycosylated site. The 'potential' score is the averaged
		           output of nine neural networks. For further information, the 'jury'
		           agreement column indicates how many of the nine networks support
		           the prediction. The final result is shown in the comment field; the
		           following values are possible:

		           for glycosylated sites:

		           +      potential>0.5
		           ++     potential>0.5 AND jury agreement (9/9)  OR potential>0.75
		           +++    potential>0.75 AND jury agreement
		           ++++   potential>0.90 AND jury agreement

		           and non-glycosylated sites:

		           -      potential<0.5
		           --     potential<0.5 AND jury agreement (all nine <0.5)
		           ---    potential<0.32 AND jury agreement

		           See http://www.cbs.dtu.dk/services/NetNGlyc/output.php for detailed
             discussion of the prediction results. Please note that this Web
		           Service only predicts on asparagines in Asn-Pro-Ser/Thr sequons;
             the interactive service mentioned above can be asked to predict on
		           all the asparagines in the input.


		CONTACT

		Questions concerning the scientific aspects of the NetPhos method should
		go to Ramneek Gupta, ramneek@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.
by rapacki (over 10 years ago)

NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. The method is described in detail in the following article:

  "Prediction of N-glycosylation site
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