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EPipe 0.921.ws0

Functional differences of protein variants


WSDL EPipe/EPipe_0_921_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_epipe_0_921_ws0.xsd

We recommend that the first time users should load the WSDL file above to SoapUI and investigate the Web Service operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP. It can be downloaded free of charge from http://www.soapui.org/.

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
simple.pl (2.4 KB) Perl 1.1 ws0 Peter Fischer Hallin
Read fasta sequences from stdin and submit to epipe
example.fsa (1.4 KB)
xml-compile.pl (3.2 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)

Documentation

    This is the Web Service implementation of the EPipe server (http://www.cbs.dtu.dk/services/EPipe)
    Input is identical to the paste-and-click version. Output is limited only to the 
    isoform alignments, feature prediction results, and the remapped coordinates of the predicted
    features mapped onto the alignment. All graphical generation is left out. The service runs asynchronously,
    split into the following three operations:
    
    1.runService 
      This operation submit sequences, alignment method plus options, and specification of which feature
      predictors to include in the run.

    INPUT
      |+ modules
      ||- mpsip       : Include PSIpred ('yes' or 'no')
      ||- mimut       : Include I-mutant ('yes' or 'no')
      ||- msig        : Include SignalP ('yes' or 'no')
      ||- mtmh        : Include TMHMM ('yes' or 'no')
      ||- mpfam       : Include PFAM ('yes' or 'no')
      ||- mpdb        : Include PDB structures ('yes' or 'no')
      ||- mpdbid      : Include PDB identity match ('yes' or 'no')
      ||- mnetph      : Include NetPhos ('yes' or 'no')
      ||- mnetog      : Include NetOGlyc ('yes' or 'no')
      |.- mnetng      : Include NetNGlyc ('yes' or 'no')
      |+ alignment
      ||- method      : Alignment method ('clustal','t-coffee','hm3align','dialign')
      ||+ clustal       (configuration parameters for alignment method 'clustal'. Used only with method 'clustal')
      |||- clgapopen  : Gap opening penalty 
      |||- clgapext   : Gap extention penalty
      |||- clendgaps  : ? penalty 
      ||.- clgapdist  : ? penalty
      ||+ t-coffee      (configuration parameters for alignment method 't-coffee'. Used only with method 't-coffee')
      | |- tgapopen   : Gap opening penalty 
      | .- tgapext    : Gap extention penalty
      .+ sequencedata
       .+ sequence      (array)
        |- id         : Identifier
        |- comment    : Optional comment identifier
        .- seq        : Identifier

    OUTPUT
      |- jobid            : The 32 byte identification string of the job
      |- datetime         : The last timepoint at which the status of the job has changed
       |- status           : Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
       |                     UNKNOWN JOBID or QUEUE DOWN
       .- expire           : Amount of hours since your job will expire

    2. pollQueue
      INPUT
        .- jobid           : The 32 byte identification string of the job
      OUTPUT
        | jobid            : The 32 byte identification string of the job
        | datetime         : The last timepoint at which the status of the job has changed
        | status           : Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED, 
        |                     UNKNOWN JOBID or QUEUE DOWN
        . expire           : Amount of hours since your job will expire

    3. fetchResult
    INTPUT
        .- jobid           : The 32 byte identification string of the job

    OUTPUT
        |+ modules           (declares details of feature predictor output)
        |.+ module           (array)
        | |- source        : Name of the feature predictor (= module)
        | .+ names          
        |  .+ name           (array)       
        |   |- color       : RGB color used for printing the feature  (*)
        |   |- description : Description of the feature
        |   |- legend      : Indicates of the feature is included in the legend of the plot (*)
        |   .- value       : Value of the feauter
        .+ entries          (container for sequence )
         .+ entry
          |- seqid         : (0 ...) indicating the sequence number in the order submitted
          |- seqname       : Name/identifier for sequnced used when submitted - seqid used is
          |                  primary identifer 
          |- aln           : The sequence in the aligned form, including gaps 
          |- seq           : The raw unaligned sequence as submitted
          |+ colors          (container for residue coloring according the clustal's default coloring scheme)
          |.- color        : (array, one element per position in the alignment)
          .+ modules  
           .+ module  
            |- source 
            .+ modules 
             .+ features 
              .+ feature
    
               |- begin       : Beginning of predicted feature, relative to orginial sequence
               |- end         : End of predicted feature, relative to orginial sequence
               |- value       : Predicted value ( see initial declaration in OUTPUT->modules
               |- begin_remap : Beginning of predicted feature, relative to aligned sequence
               .- end_remap   : End of predicted feature, relative to aligned sequence