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Other versions and implementations
|1.2.ws1|| 2012-04-10||(this version, most recent)|
Examples of client side scripts using the service
This Web Service implements NetCTL v. 1.2.ws0. 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:
Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction.
Larsen MV, Lundegaard C, Lamberth K, Buus S, Lund O, Nielsen M.
BMC Bioinformatics. Oct 31;8:424. 2007
Alongside this Web Service the NetCTL method is also implemented as
a traditional click-and-paste WWW server at:
NetCTL is also available as a stand-alone software package; write to
firstname.lastname@example.org 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:
Other users are requested to write to email@example.com for details.
WEB SERVICE OPERATION
This Web Service is fully asynchronous; the usage is split into the
following three operations:
Input: The following parameters and data:
* 'supertype' HLA supertype.
10 HLA supertypes are available:
A1, A2, A3, A24, A26, B7, B8, B27, B39, B44, B58 and B62;
* 'wtap weight on TAP transport efficiency.
The value 0.05 gives optimal predictive performance on the average;
* 'wMHC' weight on MHC;
* 'wcle' weight on C terminal cleavage.
The value 0.1 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);
* 'sequencedata' mulitple elements of type 'sequence':
* 'sequence' answers to one sequence:
* 'id' unique identifier for the sequence;
* 'comment' optional comment;
* 'seq' protein sequence. 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
Input: Unique job identifier
Output: 'jobstatus' - the status of the job
Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN
Input: Unique job identifier of a finished job
Output: * 'annsource'
'method' name of the method, here always 'NetCTL';
'version' version of the method: here always '1.2 ws0';
'ann' annotations - one element per input sequence;
'sequence' standard sequence object;
'id' sequence identifier;
'feature' feature name, here always 'NetCTL';
'range' always present, indicates the range in the sequence:
'begin' begin position;
'end' end position;
'key'='aff' predicted MHC binding affinity.
'value' score value for 'aff'. The value is given
as 1 - log50k(aff), where log50k is the
logaritm with base 50.000, and aff is the
affinity in nM units;
'key'='aff_rescale' rescale binding affinity;
'value' score value for 'aff_rescale'.
The predicted binding affinity is normalized by the 1% fractil;
'key'='cle' C terminal cleavage affinity;
'value' score value for 'cle';
'key'='tap' TAP transport efficiency;
'value' score value for 'tap';
'key'='COMB' prediction score;
'value' score value for 'COMB';
'comment' gives 'E' for identified MHC ligands (when the
combined score is greater than the threshold).
More comprehensive information about the output could be found at:
Questions concerning the scientific aspects of the NetCTL method should go
to Morten Nielsen, firstname.lastname@example.org; technical question concerning the Web
Service should go to Karunakar Bayyapu, email@example.com or Kristoffer