Web Service WSNetCTL_1_1 SOAP Dk

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Annotations: 10 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. 2

Overview

Provider:
Center for Biological Sequence Analysis (CBS)

Location:
Denmark Dk

Submitter/Source:
SeekDa (about 6 years ago)

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

WSDL Location:
http://www.cbs.dtu.dk/ws/NetCTL/NetCTL_1_1.wsdl (download last cached WSDL file)

Documentation URL(s):
None
Description(s):
from provider's description doc (about 6 years ago)
	INTRODUCTION

	This Web Service implements NetCTL v. 1.1. It predicts CTL epitopes
	in protein sequences integrating prediction of peptide MHC binding,
	proteasomal C terminal cleavage and TAP transport efficiency. The
	method is described in detail in the following article:

	An integrative approach to CTL epitope prediction. A combined
	algorithm integrating MHC-I binding, TAP transport efficiency,
	and proteasomal cleavage predictions.
	Larsen MV, Lundegaard C, Kasper Lamberth, Buus S. Brunak S,
	Lund O, and Nielsen M.
	European Journal of Immunology 35(8): 2295-303, 2005

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

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

	NetCTL is also available as a stand-alone software package; write to
	software@cbs.dtu.dk for details.
	NetCTL 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?netCTL

	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:

	        * 'supertype' - HLA supertype
	          10 HLA supertypes are available:
	          A1, A2, A3, A24, B7, B8, B27, B44, B58 and B62;

	        * 'wcle' - weight on C terminal cleavage
	          The value 0.1 gives optimal predictive performance on the average.

	        * 'wtap' - weight on TAP transport efficiency
	          The value 0.05 gives optimal predictive performance on the average.

	        * 'threshold' - threshold for epitope identification
	          Peptides with a combined prediction score value greater than the
	          threshold value are marked as potential epitopes. In a large scale
	          benchmark identifying known CTL epitope in proteins the default
	          value of 0.75 was found to correspond to a sensitivity of 0.65
	          and a specificity 0.97. Note that the benchmark is highly
	          unbalanced since only one peptide is identified as CTL epitope
	          in each protein, and the number of negatives hence is orders of
	          magnitude larger than the number of positives. This has important
	          implications for the interpretation of the specificity values.

	        * 'sort' - output sorting on score
	          Possible values are 0 (sorting on the combined score), 1 (MHC),
	          2 (Cle), 3 (TAP) and negative (no sorting)

	        * 'sequences' - protein sequences, with unique identifiers 
	          The sequence 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 12 characters in ver. 1.1a
	        source         "netCTL-1.1" (fixed string)
	        feature        "CTL" (fixed string)
	        start,end      residue number (given twice)
	        score          prediction score (combined)
	        strand,frame   N/A
	        comment        Text string consisting of:

	                       * Predicted MHC binding affinity
	                         The value is give as 1 - log50k(aff), where log50k
	                         is the logaritm with base 50.000, and aff is the
	                         affinity in nM units;
	                       * Rescaled binding affinity
	                         The predicted binding affinity is normalized by the
	                         1% fractil
	                       * C terminal cleavage affinity
	                       * TAP transport efficiency

	                       "-E" to indicate the identified MHC ligands (when
	                        the combined score is greater than the threshold).


	CONTACT

	Questions concerning the scientific aspects of the NetCTL 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.
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