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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/nucleic_gene_finding.tcode
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/nucleic_gene_finding.tcode?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/tcode.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Identify protein-coding regions using Fickett TESTCODE statistic
SoapLab Support(over 10 years ago)
Identify protein-coding regions using Fickett TESTCODE statistic
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 : tcode
- installation : Soaplab2 default installation
- type : Nucleic Gene finding
- output :
- description : Identify protein-coding regions using Fickett TESTCODE statistic
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : tcode
- installation : Soaplab2 default installation
- type : Nucleic Gene finding
- output :
- description : Identify protein-coding regions using Fickett TESTCODE statistic
- 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 : nucleic_gene_finding
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/tcode.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
- list_item :
- list :
- base :
- range :
- format : %d
- max :
- min : 200
- repeatable :
- base :
- name : window
- help : This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time. The window will then slide along the sequence, covering the same number of bases each time.
- default : 200
- option :
- name : calculated_hardmax
- type : normal
- value : ${sequence.length}
- name : scalemin
- type : style
- value : 200
- mandatory : false
- qualifier : window
- prompt : Length of sliding window
- type : long
- ordering : 6
- standard :
- list :
- list_item :
- level : 0
- shown_as : Portable Network Graphics (png)
- value : png
- level : 0
- shown_as : Postscript
- value : colourps
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : step
- help : The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive). This may be altered to increase or decrease the increment of the slide.
- default : 3
- option :
- name : calculated_hardmax
- type : normal
- value : ${sequence.length} – ${window}
- name : scalemin
- type : style
- value : 1
- mandatory : false
- qualifier : step
- prompt : Stepping increment for the window
- type : long
- ordering : 8
- base :
- name : plot
- help : On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed. Sequence above the green line is coding, that below the red line is non-coding.
- default : false
- mandatory : false
- qualifier : plot
- prompt : Graphical display
- type : boolean
- ordering : 11
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- name : Graphics_in_PNG
- option :
- 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
- mandatory : false
- qualifier : Graphics_in_PNG
- type : byte[][]
- method : %%%Graphics_in_PNG%%% ${Graphics_in_PNG}
- ordering : 13
- data :
- option :
- input :
- name : window
- default : 200
- mandatory : false
- type : long
- name : step
- default : 3
- mandatory : false
- type : long
- name : plot
- default : false
- mandatory : false
- type : boolean
- analysis :
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