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Provider:
European Bioinformatics Institute (EBI)
Location:
United Kingdom
Submitter / Source:
SoapLab Support (over 3 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/nucleic_rna_folding.vrnafold
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/nucleic_rna_folding.vrnafold?wsdl(download last cached WSDL file)
Documentation URL(s): SoapLab Support (over 2 years ago)http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/vrnafold.html
Login to add a documentation URL Description(s): from provider’s description doc (over 2 years ago) Calculate secondary structures of RNAs
SoapLab Support (over 2 years ago)Calculate secondary structures of RNAs
Login to add a description Details (from Soaplab server): from Soaplab server(over 2 years ago)
- ds_lsr_analysis :
- analysis :
- name : vrnafold
- output :
- version : 6.1.0
- type : Nucleic RNA folding, Nucleic 2D structure
- installation : Soaplab2 default installation
- description : Calculate secondary structures of RNAs
- input :
- analysis_extension :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : vrnafold
- output :
- version : 6.1.0
- type : Nucleic RNA folding, Nucleic 2D structure
- installation : Soaplab2 default installation
- description : Calculate secondary structures of RNAs
- input :
- name : temperature
- default : 37.0
- mandatory : false
- type : float
- name : circular
- default : false
- mandatory : false
- type : boolean
- name : gu
- default : false
- mandatory : false
- type : boolean
- name : closegu
- default : false
- mandatory : false
- type : boolean
- name : lp
- default : false
- mandatory : false
- type : boolean
- name : convert
- default : false
- mandatory : false
- type : boolean
- name : tetraloop
- default : false
- mandatory : false
- type : boolean
- name : scale
- default : 1.07
- mandatory : false
- type : float
- analysis_extension :
- 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
- list_item :
- list :
- base :
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- repeatable :
- base :
- ordering : 7
- name : temperature
- qualifier : temperature
- default : 37.0
- mandatory : false
- type : float
- prompt : Temperature
- base :
- ordering : 8
- name : circular
- qualifier : circular
- default : false
- mandatory : false
- type : boolean
- prompt : Allow circular RNA
- base :
- ordering : 9
- name : gu
- qualifier : gu
- default : false
- mandatory : false
- type : boolean
- prompt : Allow GU pairs
- base :
- ordering : 10
- name : closegu
- qualifier : closegu
- default : false
- mandatory : false
- type : boolean
- prompt : Allow GU pairs at end of helices
- base :
- ordering : 11
- name : lp
- qualifier : lp
- default : false
- mandatory : false
- type : boolean
- prompt : Allow lonely pairs
- base :
- ordering : 12
- name : convert
- qualifier : convert
- default : false
- mandatory : false
- type : boolean
- prompt : Convert T to U
- standard :
- repeatable :
- base :
- base :
- ordering : 14
- name : tetraloop
- qualifier : tetraloop
- default : false
- mandatory : false
- type : boolean
- prompt : Stabilizing energies for tetra-loops
- standard :
- list :
- list_item :
- shown_as : BP
- level : 0
- value : 0
- shown_as : Any with GC
- level : 0
- value : 1
- shown_as : Any with AU parameters
- level : 0
- value : 2
- name : Energy parameters
- type : full
- list_item :
- repeatable :
- list :
- base :
- range :
- format : %f
- repeatable :
- base :
- ordering : 16
- name : scale
- qualifier : scale
- default : 1.07
- mandatory : false
- type : float
- prompt : Estimate of ensemble free energy
- standard :
- list :
- list_item :
- shown_as : Ignore
- level : 0
- value : 0
- shown_as : Only unpaired bases for just one dangling end
- level : 0
- value : 1
- shown_as : Always use dangling energies
- level : 0
- value : 2
- shown_as : Allow coaxial stacking of adjacent helices
- level : 0
- value : 3
- name : How to treat dangling end energies
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- result :
- extension : ssps
- iotype : output
- base :
- data :
- 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 : nucleic_rna_folding
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/vrnafold.html
- event :
- action :
- id : _E_1
- parameter :
- analysis :
License(s): None Login to add license info Cost: No info yet Login to add cost info Usage Conditions: No info yet Login to add usage conditions info Contact Info: None Login to add contact info Publications: for this service. This can be a URI to the publication and/or a DOI. None Login to add publication info Citations: None Login to add a citation