EMBOSS needle SOAP Soaplab

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About Soaplab

Soaplab services are command line applications, wrapped as SOAP services, and served from a Soaplab server. All Soaplab services have the same generic set of SOAP operations (depending on the Soaplab version) as they all share a standardised interface.

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Further documentation on Soaplab services is available:

Provider:
European Bioinformatics Institute (EMBL-EBI)

Location:
United Kingdom

Submitter/Source:
SoapLab Support (almost 12 years ago)

Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/alignment_global.needle

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

Documentation URL(s): SoapLab Support (over 10 years ago) http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/needle.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Needleman-Wunsch global alignment of two sequences

SoapLab Support(over 10 years ago)

Needleman-Wunsch global alignment of two sequences

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 10 years ago)

  • ds_lsr_analysis :
    • analysis :
      • name : needle
      • installation : Soaplab2 default installation
      • type : Alignment Global
      • output :
      • description : Needleman-Wunsch global alignment of two sequences
      • version : 6.1.0
      • analysis_extension :
      • input :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : needle
      • installation : Soaplab2 default installation
      • type : Alignment Global
      • output :
      • description : Needleman-Wunsch global alignment of two sequences
      • version : 6.1.0
      • analysis_extension :
        • option :
          • name : emboss
          • type : normal
          • value : true
          • name : installation
          • type : normal
          • value : Soaplab2 default installation
          • name : version
          • type : normal
          • value : 6.1.0
        • event :
          • action :
          • id : _E_1
        • app_info :
          • category : alignment_global
          • help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/needle.html
        • parameter :
          • data :
            • list :
              • list_item :
                • level : 0
                • value : gcg
                • level : 0
                • value : gcg8
                • level : 0
                • value : embl
                • level : 0
                • value : swiss
                • level : 0
                • value : fasta
                • level : 0
                • value : ncbi
                • level : 0
                • value : genbank
                • level : 0
                • value : nbrf
                • level : 0
                • value : pir
                • level : 0
                • value : codata
                • level : 0
                • value : strider
                • level : 0
                • value : clustal
                • level : 0
                • value : phylip
                • level : 0
                • value : acedb
                • level : 0
                • value : msf
                • level : 0
                • value : jackknifer
                • level : 0
                • value : jackknifernon
                • level : 0
                • value : nexus
                • level : 0
                • value : nexusnon
                • level : 0
                • value : treecon
                • level : 0
                • value : mega
                • level : 0
                • value : meganon
                • level : 0
                • value : ig
                • level : 0
                • value : staden
                • level : 0
                • value : text
                • level : 0
                • value : raw
              • type : full
          • base :
          • data :
            • list :
              • list_item :
                • level : 0
                • value : gcg
                • level : 0
                • value : gcg8
                • level : 0
                • value : embl
                • level : 0
                • value : swiss
                • level : 0
                • value : fasta
                • level : 0
                • value : ncbi
                • level : 0
                • value : genbank
                • level : 0
                • value : nbrf
                • level : 0
                • value : pir
                • level : 0
                • value : codata
                • level : 0
                • value : strider
                • level : 0
                • value : clustal
                • level : 0
                • value : phylip
                • level : 0
                • value : acedb
                • level : 0
                • value : msf
                • level : 0
                • value : jackknifer
                • level : 0
                • value : jackknifernon
                • level : 0
                • value : nexus
                • level : 0
                • value : nexusnon
                • level : 0
                • value : treecon
                • level : 0
                • value : mega
                • level : 0
                • value : meganon
                • level : 0
                • value : ig
                • level : 0
                • value : staden
                • level : 0
                • value : text
                • level : 0
                • value : raw
              • type : full
          • base :
          • range :
            • format : %f
            • max : 100.0
            • min : 0.0
            • repeatable :
          • base :
            • name : gapopen
            • help : The gap open 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.
            • option :
              • name : calculated_default
              • type : normal
              • value : ${acdprotein}? 10.0 : 10.0
              • name : scalemax
              • type : style
              • value : 100.0
              • name : scalemin
              • type : style
              • value : 0.0
            • mandatory : false
            • qualifier : gapopen
            • prompt : Gap opening penalty
            • type : float
            • ordering : 7
          • range :
            • format : %f
            • max : 10.0
            • min : 0.0
            • repeatable :
          • base :
            • name : gapextend
            • help : 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. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.
            • option :
              • name : calculated_default
              • type : normal
              • value : ${acdprotein}? 0.5 : 0.5
              • name : scalemax
              • type : style
              • value : 10.0
              • name : scalemin
              • type : style
              • value : 0.0
            • mandatory : false
            • qualifier : gapextend
            • prompt : Gap extension penalty
            • type : float
            • ordering : 8
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • base :
            • name : brief
            • help : Brief identity and similarity
            • default : false
            • mandatory : false
            • qualifier : brief
            • prompt : Brief identity and similarity
            • type : boolean
            • ordering : 10
      • input :
        • name : brief
        • default : false
        • mandatory : false
        • type : boolean

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