ssematch SOAP Soaplab

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Provider:
European Bioinformatics Institute (EMBL-EBI)

Location:
UNITED KINGDOM

Submitter/Source:
Mike Mayer (over 9 years ago)

Base URL:
http://www.ebi.ac.uk/soaplab/services/utils_database_creation.ssematch

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

Documentation URL(s): None Login to add a documentation URL Description(s): No description(s) yet Login to add a description ELIXIR Description(s): No info yet Login to add an elixir description Details (from Soaplab server): from Soaplab server(over 8 years ago)

  • ds_lsr_analysis :
    • analysis :
      • name : ssematch
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : Utils Database creation
      • description : Search a DCF file for secondary structure matches.
      • analysis_extension :
      • input :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : ssematch
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : Utils Database creation
      • description : Search a DCF file for secondary structure matches.
      • analysis_extension :
        • parameter :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : maxhits
            • ordering : 7
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : This option specifies the number of top-scoring matches to report.
            • default : 5
            • qualifier : maxhits
            • mandatory : false
            • prompt : Number of top-scoring matches to report.
            • type : long
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • range :
            • format : %f
            • max : 100.
            • min : 1.
            • repeatable :
          • base :
            • name : rgapopen
            • ordering : 9
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
              • name : scalemax
              • type : style
              • value : 100.
              • name : scalemin
              • type : style
              • value : 1.
            • help : This options specifies the gap insertion penalty for reside-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.
            • default : 10
            • qualifier : rgapopen
            • mandatory : false
            • prompt : Gap insertion penalty for reside-based alignment
            • type : float
          • range :
            • format : %f
            • max : 10.
            • min : 0.0
            • repeatable :
          • base :
            • name : rgapextend
            • ordering : 10
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
              • name : scalemax
              • type : style
              • value : 10.
              • name : scalemin
              • type : style
              • value : 0.0
            • help : This options specifies the gap extension penalty for residue-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty.
            • default : 0.5
            • qualifier : rgapextend
            • mandatory : false
            • prompt : Gap extension penalty for residue-based alignment
            • type : float
          • range :
            • format : %f
            • max : 100.
            • min : 1.
            • repeatable :
          • base :
            • name : egapopen
            • ordering : 11
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
              • name : scalemax
              • type : style
              • value : 100.
              • name : scalemin
              • type : style
              • value : 1.
            • help : This options specifies the gap insertion penalty for element-based alignment. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.
            • default : 10
            • qualifier : egapopen
            • mandatory : false
            • prompt : Gap insertion penalty for secondary structure element-based alignment.
            • type : float
          • range :
            • format : %f
            • max : 10.
            • min : 0.0
            • repeatable :
          • base :
            • name : egapextend
            • ordering : 12
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
              • name : scalemax
              • type : style
              • value : 10.
              • name : scalemin
              • type : style
              • value : 0.0
            • help : This options specifies the gap extension penalty for secondary structure element-based alignment. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty.
            • default : 0.5
            • qualifier : egapextend
            • mandatory : false
            • prompt : Gap extension penalty for secondary structure element-based alignment
            • type : float
        • option :
          • name : emboss
          • type : normal
          • value : true
          • name : installation
          • type : normal
          • value : Soaplab2 default installation
          • name : version
          • type : normal
          • value : 6.3.0
        • app_info :
          • category : utils_database_creation
          • help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/ssematch.html
        • event :
          • action :
          • id : _E_1
      • input :
        • name : maxhits
        • default : 5
        • mandatory : false
        • type : long
        • name : rgapopen
        • default : 10
        • mandatory : false
        • type : float
        • name : rgapextend
        • default : 0.5
        • mandatory : false
        • type : float
        • name : egapopen
        • default : 10
        • mandatory : false
        • type : float
        • name : egapextend
        • default : 0.5
        • mandatory : false
        • type : float

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