Provider:
Center for Biological Sequence Analysis (CBS)
Location:
Denmark
Submitter/Source:
SeekDa (over 11 years ago)
Base URL:
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 (mandatory) “euk” eukaryotes “gram-” Gram-negative prokaryotes “gram+” Gram-positive prokaryotes * ‘method’ – prediction method (optional) “nn” neural network only “hmm” hidden Markov models only “nn+hmm” both methods (default) * ‘thnn’ – threshold for yes/no decision by neural nets (optional) The threshhold setting affects the ‘comment’ field in the output (see below): if the neural net score is higher that the selected threshold the comment will be “Y”, else “N”. The default thresholds are 0.43 for “euk”, 0.45 for “gram+” and 0.44 for “gram-“; the defaults have been shown to give the highest correlation coefficient on test data. Note: ‘thnn’ does not affect the signalp-hmm prediction output. * ‘sequences’ – protein sequences, with unique identifiers (mandatory) 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. Currently, at most 2,000 sequences are allowed per submission. 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-3.1-nn” or “signalp-3.1-hmm” (fixed string) ‘feature’ “signal” (fixed string) ‘start’,’end’ predicted location of the signal peptide in the sequence (0-0 is no peptide is predicted) ‘score’ prediction score: For “signalp-3.1-nn” D score, for “signalp-3.1-hmm” the signal peptide branch probability (see the article) ‘strand’ N/A ‘frame’ N/A ‘comment’ answer: For “signalp-3.1-nn” the answer is “Y” (yes) and “N” (no) depending on the selected threshold. For “signalp-3.1-hmm” the answer is “S” for signal peptide, “A” for signal anchor (“euk” only) and “Q” for none of the above. KNOWN BUGS 2007-01-30 Error handling: some error messages may be non-informative; fix in progress; 2007-01-29 The server side may time out processing large submission; temporary fix: submit not more than 2,000 sequences at a time; permanent fix in progress. CONTACT Questions concerning the scientific aspects of the SignalP method should go to Henrik Nielsen, hnielsen@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.
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