INTRODUCTION This Web Service implements NetOGlyc 3.1d.ws0. It predicts mucin type GalNAc O-glycosylation sites in mammalian proteins. The method is described in detail in the following article: "Prediction, conservation analysis and structural characterization of mammalian mucin-type O-glycosylation sites". K. Julenius, A. Moelgaard, R. Gupta and S. Brunak. Glycobiology, 15:153-164, 2005. Alongside this Web Service the NetOGlyc method is also implemented as a traditional paste-and-click WWW server at: http://www.cbs.dtu.dk/services/NetOGlyc The traditional server offers more detailed output (graphics), extended functionality and comprehensive documentation. It is suitable for close investigation of few proteins; this service is recommended for high throughput projects. NetOglyc 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?netOglyc 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: * 'signalp' run the signal peptide predictor 'signalp' on the input sequences (no value, just presence/absence). Information on the SignalP method can be found at: http://www.cbs.dtu.dk/services/SignalP/ * '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 'NetOGlyc'; 'version' version of the method: here always '3.1d ws0'; 'ann' annotations - one element per input sequence; 'sequence' standard sequence object; 'id' sequence identifier; 'annrecords/annrecord' 'feature' here always "O-glyc"; 'pos' always present, indicates the position of the residue in the sequence; 'score' 'key'='G-score' G-score: general prediction score; 'value' G-score value; 'score' 'key'='I-score' I-score: isolated site prediction score (threonine residues only); 'value' I-score value; 'comment' appears only when the residue is predicted as glycosylated, contains the letter 'T' or 'S'. It also contains 'signal peptide?' if a residue in a predicted signal peptide is predicted as glycosylated. A residue is predicted as glycosylated when the G-score for that residue is >0.5. For threonines an additional score is used: if the G-score is <0.5 but the I-score >0.5 and there are no predicted neighbouring sites (distance <10 residues) the residue is also predicted as glycosylated. CONTACT Questions concerning the scientific aspects of the NetOGlyc method should go to Ramneek Gupta, ramneek@cbs.dtu.dk; technical questions concerning the Web Service should go to Edita Bartaseviciute, edita@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.