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- Soaplab overview
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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/protein_motifs.epestfind
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/protein_motifs.epestfind?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 : epestfind
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Finds PEST motifs as potential proteolytic cleavage sites
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : epestfind
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Finds PEST motifs as potential proteolytic cleavage sites
- 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 : 2
- repeatable :
- base :
- name : window
- ordering : 6
- option :
- name : EDAM:0001251
- type : normal
- value : data Window size
- name : calculated_hardmax
- type : normal
- value : ${sequence.length}
- name : scalemin
- type : style
- value : 2
- help : Minimal distance between positively charged amino acids.
- default : 10
- qualifier : window
- mandatory : false
- prompt : Window length
- type : long
- standard :
- list :
- list_item :
- level : 0
- value : length
- level : 0
- value : position
- level : 0
- value : score
- name : Sort order of results
- type : full
- list_item :
- repeatable :
- list :
- base :
- 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 :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %3f
- max : +55.0
- min : -55.0
- repeatable :
- base :
- name : threshold
- ordering : 9
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : scalemax
- type : style
- value : +55.0
- name : scalemin
- type : style
- value : -55.0
- help : Threshold value to discriminate weak from potential PEST motifs. Valid PEST motifs are discriminated into ‘poor’ and ‘potential’ motifs depending on this threshold score. By default, the default value is set to +5.0 based on experimental data. Alterations are not recommended since significance is a matter of biology, not mathematics.
- default : +5.0
- qualifier : threshold
- mandatory : false
- prompt : Threshold score
- type : float
- base :
- name : mono
- ordering : 12
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : mono
- mandatory : false
- prompt : Use monoisotopic weights
- type : boolean
- base :
- name : potential
- ordering : 13
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Decide whether potential PEST motifs should be printed.
- default : false
- qualifier : potential
- mandatory : false
- prompt : Display potential PEST motifs
- type : boolean
- base :
- name : poor
- ordering : 14
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Decide whether poor PEST motifs should be printed.
- default : false
- qualifier : poor
- mandatory : false
- prompt : Display poor PEST motifs
- type : boolean
- base :
- name : invalid
- ordering : 15
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Decide whether invalid PEST motifs should be printed.
- default : false
- qualifier : invalid
- mandatory : false
- prompt : Display invalid PEST motifs
- type : boolean
- base :
- name : map
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Decide whether PEST motifs should be mapped to sequence.
- default : false
- qualifier : map
- mandatory : false
- prompt : Display PEST motifs map
- type : boolean
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- name : Graphics_in_PNG
- ordering : 20
- option :
- name : EDAM:0001331
- type : normal
- value : data PEST site report
- 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:0000141
- type : normal
- value : topic Proteolysis and peptide mass
- name : EDAM:0000422
- type : normal
- value : operation Protein cleavage site prediction
- 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 : protein_motifs
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/epestfind.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : window
- default : 10
- mandatory : false
- type : long
- name : threshold
- default : +5.0
- mandatory : false
- type : float
- name : mono
- default : false
- mandatory : false
- type : boolean
- name : potential
- default : false
- mandatory : false
- type : boolean
- name : poor
- default : false
- mandatory : false
- type : boolean
- name : invalid
- default : false
- mandatory : false
- type : boolean
- name : map
- default : false
- mandatory : false
- type : boolean
- analysis :
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