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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/nucleic_composition.dan
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/nucleic_composition.dan?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 : dan
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Composition
- description : Calculates nucleic acid melting temperature
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : dan
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Composition
- description : Calculates nucleic acid melting temperature
- analysis_extension :
- parameter :
- data :
- list :
- list_item :
- level : 0
- value : abi
- level : 0
- value : ace
- level : 0
- value : acedb
- level : 0
- value : bam
- level : 0
- value : biomart
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : dbid
- level : 0
- value : embl
- level : 0
- value : ensembl
- level : 0
- value : experiment
- level : 0
- value : fasta
- level : 0
- value : fastq
- level : 0
- value : fastq-illumina
- level : 0
- value : fastq-sanger
- level : 0
- value : fastq-solexa
- level : 0
- value : fitch
- level : 0
- value : gcg
- level : 0
- value : genbank
- level : 0
- value : genpept
- level : 0
- value : gff2
- level : 0
- value : gff3
- level : 0
- value : gifasta
- level : 0
- value : hennig86
- level : 0
- value : ig
- level : 0
- value : igstrict
- level : 0
- value : jackknifer
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : nexus
- level : 0
- value : pdb
- level : 0
- value : pdbnuc
- level : 0
- value : pdbnucseq
- level : 0
- value : pdbseq
- level : 0
- value : pearson
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : raw
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : stockholm
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- list_item :
- list :
- base :
- range :
- format : %d
- max : 100
- min : 1
- repeatable :
- base :
- name : windowsize
- ordering : 4
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : scalemax
- type : style
- value : 100
- name : scalemin
- type : style
- value : 1
- help : The values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window. The window is incrementally moved along the sequence with the properties being calculated at each new position.
- default : 20
- qualifier : windowsize
- mandatory : false
- prompt : Enter window size
- type : long
- range :
- format : %f
- max : 100000.
- min : 1.
- repeatable :
- base :
- name : dnaconc
- ordering : 6
- option :
- name : EDAM:0002140
- type : normal
- value : data Concentration
- name : scalemax
- type : style
- value : 100000.
- name : scalemin
- type : style
- value : 1.
- default : 50.
- qualifier : dnaconc
- mandatory : false
- prompt : Enter DNA concentration (nM)
- type : float
- range :
- format : %f
- max : 1000.
- min : 1.
- repeatable :
- base :
- name : saltconc
- ordering : 7
- option :
- name : EDAM:0002140
- type : normal
- value : data Concentration
- name : scalemax
- type : style
- value : 1000.
- name : scalemin
- type : style
- value : 1.
- default : 50.
- qualifier : saltconc
- mandatory : false
- prompt : Enter salt concentration (mM)
- type : float
- standard :
- list :
- list_item :
- shown_as : Portable Network Graphics (png)
- level : 0
- value : png
- shown_as : Postscript
- level : 0
- value : colourps
- type : full
- list_item :
- repeatable :
- list :
- base :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : shiftincrement
- ordering : 5
- option :
- name : EDAM:0002141
- type : normal
- value : data Window step size
- name : calculated_hardmax
- type : normal
- value : ${windowSize}
- name : scalemin
- type : style
- value : 1
- help : This is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence.
- default : 1
- qualifier : shiftincrement
- mandatory : false
- prompt : Enter Shift Increment
- type : long
- base :
- name : product
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This prompts for percent formamide, percent of mismatches allowed and product length.
- default : false
- qualifier : product
- mandatory : false
- prompt : Prompt for product values
- type : boolean
- range :
- format : %f
- max : 100.
- min : 0.
- repeatable :
- base :
- name : formamide
- ordering : 12
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 0.
- help : This specifies the percent formamide to be used in calculations (it is ignored unless -product is used).
- default : 0.
- qualifier : formamide
- mandatory : false
- prompt : Enter percentage of formamide
- type : float
- range :
- format : %f
- max : 100.
- min : 0.
- repeatable :
- base :
- name : mismatch
- ordering : 13
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 0.
- help : This specifies the percent mismatch to be used in calculations (it is ignored unless -product is used).
- default : 0.
- qualifier : mismatch
- mandatory : false
- prompt : Enter percent mismatch
- type : float
- range :
- format : %d
- min :
- repeatable :
- base :
- name : prodlen
- ordering : 14
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- name : calculated_default
- type : normal
- value : ${windowsize}
- name : calculated_hardmin
- type : normal
- value : ${windowsize}
- help : This specifies the product length to be used in calculations (it is ignored unless -product is used).
- qualifier : prodlen
- mandatory : false
- prompt : Enter the product length
- type : long
- base :
- name : thermo
- ordering : 17
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file.
- default : false
- qualifier : thermo
- mandatory : false
- prompt : Thermodynamic calculations
- type : boolean
- range :
- format : %f
- max : 100.
- min : 0.
- repeatable :
- base :
- name : temperature
- ordering : 18
- option :
- name : EDAM:0002139
- type : normal
- value : data Melting temperature
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 0.
- help : If -thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values.
- default : 25.
- qualifier : temperature
- mandatory : false
- prompt : Enter temperature
- type : float
- base :
- name : rna
- ordering : 22
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This specifies that the sequence is an RNA sequence and not a DNA sequence.
- default : false
- qualifier : rna
- mandatory : false
- prompt : Use RNA data values
- type : boolean
- base :
- name : plot
- ordering : 25
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced.
- default : false
- qualifier : plot
- mandatory : false
- prompt : Produce a plot
- type : boolean
- range :
- format : %f
- max : 150.
- min : 0.
- repeatable :
- base :
- name : mintemp
- ordering : 26
- option :
- name : EDAM:0002139
- type : normal
- value : data Melting temperature
- name : scalemax
- type : style
- value : 150.
- name : scalemin
- type : style
- value : 0.
- help : Enter a minimum value for the temperature scale (y-axis) of the plot.
- default : 55.
- qualifier : mintemp
- mandatory : false
- prompt : Enter minimum temperature
- type : float
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- name : Graphics_in_PNG
- ordering : 27
- option :
- name : EDAM:0002142
- type : normal
- value : data EMBOSS graph
- name : allow_non_existent
- type : normal
- value : true
- name : datatype
- type : normal
- value : bindata
- name : mimetype
- type : normal
- value : image/png
- name : nodisplay
- type : style
- value : true
- method : %%%Graphics_in_PNG%%% ${Graphics_in_PNG}
- qualifier : Graphics_in_PNG
- mandatory : false
- type : byte[][]
- data :
- option :
- name : EDAM:0000104
- type : normal
- value : topic Nucleic acid denaturation
- name : EDAM:0000455
- type : normal
- value : operation Nucleic acid melting temperature calculation
- 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 : nucleic_composition
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/dan.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : windowsize
- default : 20
- mandatory : false
- type : long
- name : dnaconc
- default : 50.
- mandatory : false
- type : float
- name : saltconc
- default : 50.
- mandatory : false
- type : float
- name : shiftincrement
- default : 1
- mandatory : false
- type : long
- name : product
- default : false
- mandatory : false
- type : boolean
- name : formamide
- default : 0.
- mandatory : false
- type : float
- name : mismatch
- default : 0.
- mandatory : false
- type : float
- name : thermo
- default : false
- mandatory : false
- type : boolean
- name : temperature
- default : 25.
- mandatory : false
- type : float
- name : rna
- default : false
- mandatory : false
- type : boolean
- name : plot
- default : false
- mandatory : false
- type : boolean
- name : mintemp
- default : 55.
- mandatory : false
- type : float
- analysis :
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