INTRODUCTION This Web Service implements ProP v. 1.0.ws0. It predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. The method is described in detail in the following article: Prediction of proprotein convertase cleavage sites. Peter Duckert, Soren Brunak and Nikolaj Blom. Protein Engineering, Design and Selection: 17: 107-112, 2004. Alongside this Web Service the ProP method is also implemented as a traditional paste-and-click WWW server at: http://www.cbs.dtu.dk/services/ProP/ The traditional server offers extended functionality and comprehensive documentation. It is suitable for close investigation of few proteins; this service is recommended for high throughput projects. 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 * 'sequenceRecord' answers to one sequence: * 'sequence' protein sequence. The sequence must be written using the one letter amino acid code in capital letters: `ACDEFGHIKLMNPQRSTVWY'.Other letters will be converted to `X' and treated as unknown amino acids. Other symbols, such as whitespace and numbers, will be ignored; * 'customNote' optional comment; * 'formalReference' * 'accession' unique identifier for the sequence. 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: * 'annotatedSequence' annotations - one element per input sequence; * 'sequenceRecord' answers to one sequence: * 'sequence' protein sequence given as an input; * 'formalReference' * 'accession' unique identifier for the input sequence; * 'annotation' * 'feature' * 'name' feature name, here always 'ProP'; * 'occurence' occurence of a feature in a sequence; * 'position' always present, indicates the position for each arginine (R) and lysine (K) residue in the sequence; * 'point' residues number; * 'evidence' * 'predicted' * 'methodId' id composed of today's day, name and version of the method. Example: 6-4-2010ProP-1.0ws0; * 'score' * 'type' score type name, here always 'main', indicating the main prediction score; * 'value' prediction score value. If the score is >0.5 the residue is predicted to be followed by a propeptide cleavage site; the higher the score the more confident the prediction; * 'verdict' contains 'Present' if the residue is predicted to be followed by a propeptide cleavage site, and 'Impossible' if the residue is not predicted to be followed by a propeptide cleavage site. Please note, that input and output data types of the ProP v. 1.0.ws0 Web Service are defined by the external canonical BioXSD XML-Schema. CONTACT Technical questions concerning the Web Service should go to Edita Bartaseviciute,edita@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.