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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.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
More information on Soaplab clients is available here.
Further documentation on Soaplab services is available:
- Soaplab overview
- Soaplab client guide page
- EBI Soaplab server documentation
- Soaplab 2
- Sourceforge site for EMBOSS Soaplab services
Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
United Kingdom
Submitter/Source:
SoapLab Support (over 11 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/utils_database_creation.ssematch
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/utils_database_creation.ssematch?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/ssematch.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Search a DCF file for secondary structure matches.
SoapLab Support(over 10 years ago)
Search a DCF file for secondary structure matches.
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 : ssematch
- installation : Soaplab2 default installation
- type : Utils Database creation
- output :
- description : Search a DCF file for secondary structure matches.
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : ssematch
- installation : Soaplab2 default installation
- type : Utils Database creation
- output :
- description : Search a DCF file for secondary structure matches.
- 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 : utils_database_creation
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/ssematch.html
- parameter :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : maxhits
- help : This option specifies the number of top-scoring matches to report.
- default : 5
- mandatory : false
- qualifier : maxhits
- prompt : Number of top-scoring matches to report.
- type : long
- ordering : 7
- 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
- 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
- option :
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 1.
- mandatory : false
- qualifier : rgapopen
- prompt : Gap insertion penalty for reside-based alignment
- type : float
- ordering : 9
- range :
- format : %f
- max : 10.
- min : 0.0
- repeatable :
- base :
- name : rgapextend
- 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
- option :
- name : scalemax
- type : style
- value : 10.
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : rgapextend
- prompt : Gap extension penalty for residue-based alignment
- type : float
- ordering : 10
- range :
- format : %f
- max : 100.
- min : 1.
- repeatable :
- base :
- name : egapopen
- 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
- option :
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 1.
- mandatory : false
- qualifier : egapopen
- prompt : Gap insertion penalty for secondary structure element-based alignment.
- type : float
- ordering : 11
- range :
- format : %f
- max : 10.
- min : 0.0
- repeatable :
- base :
- name : egapextend
- 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
- option :
- name : scalemax
- type : style
- value : 10.
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : egapextend
- prompt : Gap extension penalty for secondary structure element-based alignment
- type : float
- ordering : 12
- data :
- option :
- 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
- analysis :
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