Center for Biological Sequence Analysis (CBS)


SeekDa (over 11 years ago)

Base URL: 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: ‘graphics’ OPTIONAL. Can be ‘yes’ or ‘no’ indicating whether or not graphical output should be added to the output. PLEASE BE AWARE that this option adds significant compute time and it is therefor advised to apply this to smaller datasets (50-100 proteins). For larger data sets, an initial run can be submitted without graphical output, and a job can subsequently be submitted based on the filtered results for the first run, now including graphics. ‘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 sequence a record is output consisting of the following fields: ‘len’ The length of the protein sequence ‘PredHel’ The number of predicted transmembrane helices. ‘ExpAA’ The expected number of amino acids intransmembrane helices. If this number is larger than 18 it is very likely to be a transmembrane protein (OR have a signal peptide). ‘First60’ The expected number of amino acids in transmembrane helices in the first 60 amino acids of the protein. If this number more than a few, you should be warned that a predicted transmembrane helix in the N-term could be a signal peptide. ‘NinProb’ The total probability that the N-term is on the cytoplasmic side of the membrane. ‘NtermSignal’ (yes/no) A warning that is produced when ‘First60’ is larger than 10. ‘image’ OPTIONAL – common image data type, base64 encoded PNG image ‘comment’ Fixed: Posterior probabilities of inside/outside/TM helix ‘encoding’ Fixed: base64 ‘MIMEtype’ Fixed: image/png ‘content’ Base64 encoded image: iVBORw0KGgoAAAANS… ‘topology’ The topology of the helix prediction: ‘location’ (inside/outside) ‘begin’ Start postion ‘end’ End position VERSIONS 2.0 : initial 2.0b : A change was made to version 2.0b to use a different service endpoint (simple.cgi instead of server.cgi). The change is transparent to the to the user. CONTACT Questions concerning the scientific aspects of the TMHMM method should go to Anders Krogh,; technical questions concerning the Web Service should go to Peter Fischer Hallin, or Kristoffer Rapacki,

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