EMBOSS rocon SOAP Soaplab

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Provider:
European Bioinformatics Institute (EBI)

Location:
United Kingdom

Submitter / Source:
uludag (over 2 years ago)

Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/protein_3d_structure.rocon

WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/protein_3d_structure.rocon?wsdl(download last cached WSDL file)

Documentation URL(s): uludag (about 1 year ago)http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/rocon.html

Login to add a documentation URL Description(s): from provider’s description doc (10 months ago) Generates a hits file from comparing two
DHF files

Franck Tanoh (about 1 year ago)Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a domain families file (validation sequences of known classification) and writes a “hits file” for the hits, which are classified and rank-ordered on the basis of score

uludag (about 1 year ago)Generates a hits file from comparing two DHF files.

Login to add a description Details (from Soaplab server): from Soaplab server(10 months ago)

  • ds_lsr_analysis :
    • analysis :
      • name : rocon
      • output :
      • version : 6.1.0
      • type : Protein 3D Structure
      • installation : Soaplab2 default installation
      • description : Generates a hits file from comparing two DHF files
      • input :
      • analysis_extension :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : rocon
      • output :
      • version : 6.1.0
      • type : Protein 3D Structure
      • installation : Soaplab2 default installation
      • description : Generates a hits file from comparing two DHF files
      • input :
        • name : thresh
        • default : 10
        • mandatory : false
        • type : long
      • analysis_extension :
        • parameter :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • range :
            • format : %d
            • repeatable :
          • base :
            • ordering : 5
            • name : thresh
            • help : This option specifies the overlap threshold for hits. This is the minimum length (residues) of overlap required for two hits with the accession number to be counted as the same hit. The accession number of the hit, and the start and end point respectively of the hit relative to full length sequence are provided in the lists of hits in the DHF input file. The overlap is determined from the start and end points of the hit. For example two hits with the start and end points of 1-100 and 91-190 respectively are considered to be the same hit if they have the same accession numbers and the overlap threshold is 10 or less.
            • qualifier : thresh
            • default : 10
            • mandatory : false
            • type : long
            • prompt : Overlap threshold for hits.
          • standard :
            • list :
              • list_item :
                • shown_as : Family classification scheme
                • level : 0
                • value : 1
                • shown_as : (Not yet available)
                • level : 0
                • value : 2
              • name : Classification scheme to use
              • type : full
            • repeatable :
          • base :
          • data :
            • result :
            • extension : dhf
            • iotype : output
          • base :
        • option :
          • name : emboss
          • value : true
          • type : normal
          • name : installation
          • value : Soaplab2 default installation
          • type : normal
          • name : version
          • value : 6.1.0
          • type : normal
        • app_info :
          • category : protein_3d_structure
          • help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/rocon.html
        • event :
          • action :
          • id : _E_1

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