INTRODUCTION 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 Edita Karosiene, edita@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.