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About Soaplab
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- Soaplab overview
- Soaplab client guide page
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- Soaplab 2
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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_cpg_islands.cpgplot
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/nucleic_cpg_islands.cpgplot?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 : cpgplot
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic CpG Islands
- description : Identify and plot CpG islands in nucleotide sequence(s)
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : cpgplot
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic CpG Islands
- description : Identify and plot CpG islands in nucleotide sequence(s)
- 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 :
- min : 1
- repeatable :
- base :
- name : window
- ordering : 4
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : calculated_hardmax
- type : normal
- value : ${sequence.end}
- name : scalemin
- type : style
- value : 1
- help : The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter. The window is moved down the sequence and these statistics are calculated at each position that the window is moved to.
- default : 100
- qualifier : window
- mandatory : false
- prompt : Window size
- type : long
- range :
- format : %f
- max : 10.
- min : 0.
- repeatable :
- base :
- name : minoe
- ordering : 6
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : scalemax
- type : style
- value : 10.
- name : scalemin
- type : style
- value : 0.
- help : This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported.
- default : 0.6
- qualifier : minoe
- mandatory : false
- prompt : Minimum observed/expected
- type : float
- range :
- format : %f
- max : 100.
- min : 0.
- repeatable :
- base :
- name : minpc
- ordering : 7
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : scalemax
- type : style
- value : 100.
- name : scalemin
- type : style
- value : 0.
- help : This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported.
- default : 50.
- qualifier : minpc
- mandatory : false
- prompt : Minimum percentage
- type : float
- data :
- result :
- iotype : output
- base :
- 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 :
- data :
- result :
- iotype : output
- base :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : minlen
- ordering : 5
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- name : calculated_hardmax
- type : normal
- value : ${sequence.end}
- name : scalemin
- type : style
- value : 1
- help : This sets the minimum length that a CpG island has to be before it is reported.
- default : 200
- qualifier : minlen
- mandatory : false
- prompt : Minimum length of an island
- type : long
- base :
- name : plot
- ordering : 11
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : plot
- mandatory : false
- prompt : Plot CpG island score
- type : boolean
- base :
- name : obsexp
- ordering : 13
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed.
- default : false
- qualifier : obsexp
- mandatory : false
- prompt : Show observed/expected threshold line
- type : boolean
- base :
- name : cg
- ordering : 14
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed.
- default : false
- qualifier : cg
- mandatory : false
- prompt : Show CpG rich regions
- type : boolean
- base :
- name : pc
- ordering : 15
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set to true then the graph of the percentage C plus G within a window is displayed.
- default : false
- qualifier : pc
- mandatory : false
- prompt : Show percentage line
- type : boolean
- standard :
- list :
- list_item :
- level : 0
- value : gff
- level : 0
- value : gff2
- level : 0
- value : embl
- level : 0
- value : genbank
- level : 0
- value : ddbj
- level : 0
- value : pir
- level : 0
- value : swiss
- level : 0
- value : dasgff
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- name : Graphics_in_PNG
- ordering : 12
- 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:0000157
- type : normal
- value : topic Sequence composition
- name : EDAM:0000430
- type : normal
- value : operation CpG island and isochores identification
- name : EDAM:0000576
- type : normal
- value : operation CpG island and isochores visualisation
- 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_cpg_islands
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cpgplot.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : window
- default : 100
- mandatory : false
- type : long
- name : minoe
- default : 0.6
- mandatory : false
- type : float
- name : minpc
- default : 50.
- mandatory : false
- type : float
- name : minlen
- default : 200
- mandatory : false
- type : long
- name : plot
- default : false
- mandatory : false
- type : boolean
- name : obsexp
- default : false
- mandatory : false
- type : boolean
- name : cg
- default : false
- mandatory : false
- type : boolean
- name : pc
- default : false
- mandatory : false
- type : boolean
- analysis :
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