Web Service WSNetChop_3_1 SOAP

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This service has been archived because it may not be active anymore (or is close to being non active).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 NetChop - Prediction of proteasomal cleavages (MHC ligands) aka NetChop Add_annotation_inactiveAdd_annotation_inactiveLog in to add alternative_name
UNCHECKED
Annotations: 19 Total number of annotations from the provider's definition / description document. 1 Total number of annotations submitted by members of BioCatalogue. 10 Total number of annotations sourced from other registries. 8

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
European Union

Submitter/Source:
Franck TanohGb (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/NetChop/NetChop_3_1.wsdl (download last cached WSDL file)

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

	This Web Service implements NetChop v. 3.1. It produces neural network
	predictions for cleavage sites of the human proteasome. The method is
	described in detail in the following article:

	The role of the proteasome in generating cytotoxic T cell epitopes:
	Insights obtained from improved predictions of proteasomal cleavage.
	M Nielsen, C Lundegaard, O Lund, and C Kesmir.
	Immunogenetics., 57(1-2):33-41, 2005.

	Alongside this Web Service the NetChop method is also implemented as
	a traditional click-and-paste WWW server at:
  
	  http://www.cbs.dtu.dk/services/NetChop/
    
	NetChop 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?netchop

	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:

	        * 'method' - prediction method
                  0 for "C term 3.0", 1 for "20S 3.0";

	        * 'threshold' - threshold for yes/no decision
	          The default is 0.5; increasing the threshold results in better
	          specificity, but worse sensitivity

	        * '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.

	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        truncated to 10 characters in ver. 3.1a
	        source         "netchop-3.1a" (fixed string)
	        feature        "cleavage" (fixed string)
	        start,end      residue number (given twice)
	        score          prediction score
	        strand,frame   N/A
	        comment        answer ("S" for yes, "." for no)


	CONTACT

	Questions concerning the scientific aspects of the NetChop method should go
	to Morten Nielsen, mniel@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.
by Franck Tanoh (over 11 years ago)

Predict cleavage sites of the human proteasome. interface: http://www.cbs.dtu.dk/services/NetChop/

by The EMBRACE Registry (over 11 years ago)

NetChop produces neural network predictions for cleavage sites of the human proteasome. The method is described in detail in the following article:

The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained from improved predic

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