INTRODUCTION This Web Service implements NetPhos v. 3.1b.ws0. It predicts serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins using ensembles of neural networks. Both generic and kinase specific predictions are performed. The method is described in detail in the following articles. Generic predictions: "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". Blom N, Gammeltoft S, Brunak S (1999). J Mol Biol. 1999 Dec 17;294(5):1351-62. Kinase specific predictions: "Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence". Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S (2004). Proteomics. 2004 4(6):1633-49. Review. Alongside this Web Service the NetPhos method is also implemented as two traditional paste-and-click WWW servers at: http://www.cbs.dtu.dk/services/NetPhos/ (generic predictions) http://www.cbs.dtu.dk/services/NetPhosK/ (kinase specific predictions) The traditional servers offer more detailed output (graphics), extended functionality and comprehensive documentation. They are suitable for close investigation of few proteins; this service is recommended for high throughput projects. NetPhos 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?netphos 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 * 'ser' Predict only on the S (serine) residues (no value, just presence/absence); OR * 'thr' Predict only on the T (threonine) residues (no value, just presence/absence); OR * 'tyr' Predict only on the Y (tyrosine) residues (no value, just presence/absence); * 'genericPred' Run generic predictions only, as in NetPhos 2.0 (no value, just presence/absence). Information on the NetPhos-2.0 can be found at: http://www.cbs.dtu.dk/services/NetPhos-2.0/ * 'bestScore' Report only the best (highest) score for each residue (no value, just presence/absence); * 'kinaseSpec' Run kinase specific predictions only, as in NetPhosK 1.0 (no value, just presence/absence). Information on the NetPhosK 1.0 can be found at: http://www.cbs.dtu.dk/services/NetPhosK-1.0/ * 'cutoff' Report only the scores higher than cutoff. Choosing 0.5 implies reporting only the predicted sites. * '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 'NetPhos'; 'version' version of the method: here always '3.1b ws0'; 'ann' annotations - one element per input sequence; 'sequence' standard sequence object; 'id' sequence identifier; 'annrecords/annrecord' 'feature' active kinase ('unsp' for generic predictions); 'pos' always present, indicates the position of the residue in the sequence; 'score' 'key' score key name, here always 'main', indicating the main prediction score; 'value' prediction score value, if higher than 0.5 the residue is a predicted phosphorylation site, the higher the score the more secure the prediction; 'comment' appears only when the score is higher than 0.5, contains the word 'YES'. CONTACT Questions concerning the scientific aspects of the NetPhos method should go to Thomas Sicheritz, thomas@cbs.dtu.dk; technical questions concerning the Web Service should go to Karunakar Bayyapu, karun@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.