INTRODUCTION This Web Service implements NetChop v. 3.1.ws0. 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; * '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 'NetChop'; 'version' version of the method: here always '3.1 ws0'; 'ann' annotations - one element per input sequence; 'sequence' standard sequence object; 'id' sequence identifier; 'annrecords/annrecord' 'feature' feature name, here always 'NetChop'; 'pos' always present, indicates the position in the sequence; 'score' 'key' score key name, here always 'main', indicating the main prediction score; 'value' prediction score value; 'comment' gives 'S' for identified cleavage sites. Appears only if the prediction score is greater than the threshold. 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 Karunakar Bayyapu, karun@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.