INTRODUCTION This Web Service implements SignalP v. 3.0. It predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks and hidden Markov models. The method is described in detail in the following article: Improved prediction of signal peptides: SignalP 3.0. J D Bendtsen, H Nielsen, G v Heijne and S Brunak. J. Mol. Biol., 340:783-795, 2004. Alongside this Web Service the SignalP method is also implemented as a traditional click-and-paste WWW server at: http://www.cbs.dtu.dk/services/SignalP/ 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. SignalP is also available as a stand-alone software package; 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: * 'organism' - organism type of the input sequences "euk" eukaryotes "gram-" Gram-negative prokaryotes "gram+" Gram-positive prokaryotes * 'method' - prediction method "nn" neural network only "hmm" hidden Markov models only "nn+hmm" both methods (the default) * 'sequences' - protein sequences, with unique identifiers The sequences 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. All the input sequences are truncated to 70 aa from the N-terminal. At most 2,000 sequences and 200,000 amino acids per submission; each sequence not more than 6,000 amino acids. 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: 'output' - prediction results For each input residue a record is output consisting of the following fields: seqname sequence name source "signalp-3.0-nn" or "signalp-3.0-hmm" (fixed string) feature "signal" (fixed string) start,end predicted position of the signal peptide in the sequence (0-0 is no peptide is predicted) score prediction score (D score, see the article) strand,frame N/A comment answer ("Y" or "S" for yes, "n" or "Q" for no) CONTACT Questions concerning the scientific aspects of the SignalP method should go to Henrik Nielsen, hnielsen@cbs.dtu.dk; technical question concerning the Web Service should go to Peter Fischer Hallin, pfh@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.