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RNAmmer 1.2.ws1

Prediction of ribosomal RNA sub units


WSDL RNAmmer/RNAmmer_1_2_ws1.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_rnammer_1_2_ws1.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
rnammer_php (4.5 KB) PHP 1.2 ws1 Karunakar Bayyapu
Client script in PHP running the RNAmmer Web Service
rnammer_csharp (5.5 KB) C# 1.2 ws1 Karunakar Bayyapu
Client script in C# (mono) running the RNAmmer Web Service
rnammer_perl1 (5.6 KB) Perl 1.2 ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the RNAmmer Web Service
rnammer_soap_analysis (8.3 KB) 1.2 ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
rnammer_java (6.5 KB) Java 1.2 ws1 Karunakar Bayyapu
Client script in Java (apache) running the RNAmmer Web Service
getseq.pl (973 B) Perl Genome Atlas 3.0.ws2 Peter Fischer Hallin
Download genome sequence of a genbank accession no.
rnammer.pl (2.1 KB) Perl 1.2 ws0 Peter Fischer Hallin
Reads a genomic sequence from STDIN and submits to RNAMmer to predict rRNA genes
rnammer_perl2 (5.4 KB) Perl 1.2 ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the RNAmmer Web Service
rnammer_python (4.9 KB) Python 1.2 ws1 Karunakar Bayyapu
Client script in Python (suds) running the RNAmmer Web Service
xml-compile.pl (3.2 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
fasta.inc.pl (877 B) Perl NA Peter Fischer Hallin
Helper script to parse input fasta file

Documentation

    INTRODUCTION
    
    This Web Service predicts location of ribosomal RNA genes in full genome sequences
  by using Hidden Markov Models based on alignments from a highly cureated dataset of 
  structurally aligned sequnces.
  
  The input is one or more genomic sequence(s) as either one or more contigs. Each contig
  is submitted as one continous string of DNA together with the sequences identifier.
  
  The kingdom (either Bacteria, Archaea, or Eukaryotes) is specified once for each job 
  that is submitted, using the abbriviations 'bac', 'arc', and 'euk'.

    More information about the method can be found at:
  
       http://www.cbs.dtu.dk/services/RNAmmer/

  This service is fully asynchronous;  the usage is split into the following
  three operations, which is usually executed in this order.
  
  Procedures and messages used are either common and shared among all the CBS
  Web Services, or distinct to each individual Web Service. Marked [distinct] and
  [common] respectively.

  1. runService [distinct/common]
    Submit the input parapeter(s) and sequence data and returns a job identifier

    Input: [distinct]
          * 'mol' -Molecule (e.g. ssu,lsu,tsu)
          * 'kingdom' - The kingdom of the genomic sequence
            3 kingdoms are available: bac, euk, arc. This is specified
            only once for the sequences in the current job.
          * 'sequences' - An array of sequence objects, containing the following elements:
           *  'ident' - The identifier of the sequence
           *  'seq' - The sequence specified as one continous string
    Output: [common]
          * '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
    
  2. pollQueue [common]
  Once obtained from 'runService', a job identification can be used to poll the
  status to see if the result is ready for download.

    Input:   [common]
          * 'jobid' - The 32 byte identification string of the job
    Output:  [common]
          * '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

  3. fetchResult  [distinct/common]
  Once the status is 'FINISHED' the results generated by the Web Service can be retrieved by
  specifying the jobid;
  
    Input:   [common]
          * 'jobid' - The 32 byte identification string of the job
    Output:  [distinct]
          *  'predictionTitle' - Short description of the generated output
          *  'predictor' - Name and version of the program which generated the output
          *  'predictionDate' - Date at the time the when the prediction finished
          *  'entries' - A collection of gene predictions containing the following information:
           *    'mol' - Molecule type (5/8s, 16/18s, or 23/28s rRNA) 
           *    'feature' - feature type (rRNA)
           *    'start' - Start position of the gene (integer)
           *    'stop' - stop position of the gene (integer)
           *    'direction' - strand of the gene (+/-)
           *    'score' - The HMM alignment score (floating point number)
           *    'evalue' - The E-value of the HMM alignment  (floating point number)
           *    'sequenceEntry' - The sequence identifier ( as specified when sequence 
                 was uploaded )
           *    'sequence' - The gene sequence extracted from the genomic contig
           *    'model_string' - The consensus of the Hidden Markov Model (output from hmmsearch)
           *    'match_string' - The match of the query to the model (output from hmmsearch)
           *    'query_string' - The query sequence (output from hmmsearch)
          
    For more information, please contact Peter F. Hallin: pfh@cbs.dtu.dk

    The method is described in the following paper:
    RNAmmer: consistent and rapid annotation of ribosomal RNA genes (2007) Karin Lagesen, 
    Peter Fischer Hallin, and David W. Ussery
    
    
    CONTACT

    Technical questions concerning the Web Service should go to Karunakar Bayyapu, karun@cbs.dtu.dk 
    or Kristoffer Rapacki, rapacki@cbs.dtu.dk.