INTRODUCTION This Web Service implements NetNGlyc 1.0b. It predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. The method is described in detail in the following article: "Prediction of N-glycosylation sites in human proteins". R. Gupta, E. Jung and S. Brunak. In preparation, 2004. Alongside this Web Service the NetNGlyc method is also implemented as a traditional interactive WWW server at: http://www.cbs.dtu.dk/services/NetNGlyc The traditional server offers more detailed output (graphics), extended functionality and comprehensive documentation. It is suitable for close investigation of few proteins while this service is recommended for high throughput projects. NetNglyc 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?netNglyc 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: An object of the type 'sequencedata' (see the complete definition in http://www.cbs.dtu.dk/ws/common/ws_common_1_0a.xsd) holding protein sequences with mandatory unique identifiers. Each 'sequence' is a pair of 'id' (identifier) and 'seq' (sequence itself). The sequences must be written in 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: An object of the type 'anndata' (see the complete definition in http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd) holding the predition results. 'annsource' states the 'method' (in this case always 'netNglyc') and 'version' (in this case 3.1b). The objects of the type 'annrecord' hold the predictions for a given residue in a given sequence, the fields are: feature - always "N-glyc"; pos - sequence residue; score - 'potential': N-glycosylation potential; score - 'jury': jury agreement (see below); comment - prediction result (see below). The two scores above should be interpreted as follows: Any potential crossing the default threshold of 0.5, represents a predicted glycosylated site. The 'potential' score is the averaged output of nine neural networks. For further information, the 'jury' agreement column indicates how many of the nine networks support the prediction. The final result is shown in the comment field; the following values are possible: for glycosylated sites: + potential>0.5 ++ potential>0.5 AND jury agreement (9/9) OR potential>0.75 +++ potential>0.75 AND jury agreement ++++ potential>0.90 AND jury agreement and non-glycosylated sites: - potential<0.5 -- potential<0.5 AND jury agreement (all nine <0.5) --- potential<0.32 AND jury agreement See http://www.cbs.dtu.dk/services/NetNGlyc/output.php for detailed discussion of the prediction results. Please note that this Web Service only predicts on asparagines in Asn-Pro-Ser/Thr sequons; the interactive service mentioned above can be asked to predict on all the asparagines in the input. CONTACT Questions concerning the scientific aspects of the NetPhos method should go to Ramneek Gupta, ramneek@cbs.dtu.dk; technical questions concerning the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.