NetMHCcons 1.0.ws1Prediction of binding of peptides to any known MHC class I molecule
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Documentation
This Web Service implements NetMHCcons v. 1.0.ws0. It predicts binding
of peptides to any known MHC class I molecule. This is a consensus method for
MHC class I predictions integrating three state-of-the-art methods NetMHC,
NetMHCpan and PickPocket to give the most accurate predictions.
http://www.cbs.dtu.dk/services/NetMHCcons/abstract.php
Alongside this Web Service the NetMHCcons method is also implemented as
a traditional click-and-paste WWW server at:
http://www.cbs.dtu.dk/services/NetMHCcons/
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:
* 'allele' MHC class I allele which you want to get the predictions for.
See the list of available alleles:
http://www.cbs.dtu.dk/services/NetMHCcons/MHC_allele_names.txt
* 'sort' Output sorting by descending predicted binding affinity (just present or absent);
* 'length' Peptide length between 8 and 11 amino acids. Several lengths are
possible and should be specified separated by comas (i.e.'8,9');
* 'method' Method which you want to use for predictions. Possible values are 'NetMHC', 'NetMHCpan'
'PickPocket' and 'NetMHCcons' (which is the default method).Note that using NetMHC method,
the list of possible alleles becomes shorter:
http://www.cbs.dtu.dk/services/NetMHCcons/MHC_allele_names_NetMHC.txt
* 'rankS' Threshold for Strong binding peptides expressed as %Rank;
* 'rankW' Threshold for Weak binding peptides expressed ad %Rank;
* 'affS' Threshold for Strong binding peptides expressed as IC50 value;
* 'affS' Threshold for Weak binding peptides expressed as IC50 value;
* '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
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: * 'annsource'
'method' name of the method, here always 'NetMHCcons';
'version' version of the method: here always '1.0 ws0';
'ann' annotations - one element per input sequence;
'sequence' standard sequence object;
'id' sequence identifier;
'annrecords/annrecord'
'feature' allele name;
'range' always present, indicates the range in the sequence:
'begin' begin position of the peptide;
'end' end position of the peptide;
'score'
'key'='log_score' prediction score;
'value' score value for 'log_score'. 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;
'score'
'key'='aff' predicted binding affinity;
'value' score value for 'aff'. The predicted
binding affinity as IC50 value in nM;
'score'
'key'='rank' %Rank;
'value' score value for 'rank'. % Rank of prediction score
to a set of 200.000 random natural 9mer peptides
'comment' gives 'SB' for identified strong binders and 'WB'
for identified weak binders. The peptide will be
identified as a strong binder if the % Rank OR
binding affinity (IC50) is below the specified
threshold for the strong binders. The peptide will
be identified as a weak binder if the % Rank OR
binding affinity (IC50) is above the threshold
of the strong binders but below the specified
threshold for the weak binders
More comprehensive information about the output could be found at:
http://www.cbs.dtu.dk/services/NetMHCcons/output.php
CONTACT
Questions concerning the scientific aspects of the NetMHCcons method should go
to Morten Nielsen, mniel@cbs.dtu.dk or Edita Karosiene edita@cbs.dtu.dk.
Technical question concerning the Web Service should go to
Karunakar Bayyapu, karun@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.
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