Web Service WSNetPhos_3_1b SOAP Dk

Cog_error Archived / Deprecated

This service has been archived because it may not be active anymore (or is close to being non active).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

aka NetPhos - Prediction of generic phosphorylation sites in eukaryotic proteins Add_annotation_inactiveAdd_annotation_inactiveLog in to add alternative_name
UNCHECKED
Annotations: 24 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 11 Total number of annotations sourced from other registries. 12

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/simple.cgi

WSDL Location:
http://www.cbs.dtu.dk/ws/NetPhos/NetPhos_3_1b.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 NetPhos 3.1b. It predicts serine, threonine
		and tyrosine phosphorylation sites in eukaryotic proteins using ensembles
		of neural networks. Both generic and kinase specific predictions are
		performed. The method is described in detail in the following articles.

		Generic predictions:

		"Sequence and structure-based prediction of eukaryotic protein
		phosphorylation sites".
		Blom N, Gammeltoft S, Brunak S (1999). 
		J Mol Biol. 1999 Dec 17;294(5):1351-62.

		Kinase specific predictions:

		"Prediction of post-translational glycosylation and phosphorylation
		of proteins from the amino acid sequence".
		Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004).  
		Proteomics. 2004 4(6):1633-49. Review.

		Alongside this Web Service the NetPhos method is also implemented as
		two traditional paste-and-click WWW servers at:

		    http://www.cbs.dtu.dk/services/NetPhos/  (generic predictions)
		    http://www.cbs.dtu.dk/services/NetPhosK/ (kinase specific predictions)

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

		NetPhos 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?netphos

		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_0b.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 'netphos') 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       - active kinase ('unsp' for generic predictions);
		           pos           - sequence residue;
		           score         - prediction score, if higher than 0.5 the residue
		                           is a predicted phosphorylation site, the higher
		                           the score the more secure the prediction;
		           comment       - appears only when the score is higher than 0.5,
		                           contains the word 'YES'.


		CONTACT

		Questions concerning the scientific aspects of the NetPhos method should
		go to Thomas Sicheritz, thomas@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 The EMBRACE Registry (over 11 years ago)

NetPhos predicts serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. The method is described in detail in the following articles.

Gene

ELIXIR Description(s): Info
No info yet
License(s): Info
No info yet
Cost: Info
No info yet
Usage conditions: Info
No info yet
Contact info: Info
No info yet
How to cite this service: Info
No info yet
Publications about this service: Info
No info yet
Citations of this service: Info
No info yet

Info Members Responsible for this Service (0)

No one

Info Favourited By (0)

No one

Info Similar Services (100)