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About Soaplab
Soaplab services are command line applications, wrapped as SOAP services, and served from a Soaplab server. All Soaplab services have the same generic set of SOAP operations (depending on the Soaplab version) as they all share a standardised interface.
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More information on Soaplab clients is available here.
Further documentation on Soaplab services is available:
- Soaplab overview
- Soaplab client guide page
- EBI Soaplab server documentation
- Soaplab 2
- Sourceforge site for EMBOSS Soaplab services
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.digest
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/protein_motifs.digest?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 : digest
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Reports on protein proteolytic enzyme or reagent cleavage sites
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : digest
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Reports on protein proteolytic enzyme or reagent 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 :
- standard :
- list :
- list_item :
- shown_as : Trypsin
- level : 0
- value : 1
- shown_as : Lys-C
- level : 0
- value : 2
- shown_as : Arg-C
- level : 0
- value : 3
- shown_as : Asp-N
- level : 0
- value : 4
- shown_as : V8-bicarb
- level : 0
- value : 5
- shown_as : V8-phosph
- level : 0
- value : 6
- shown_as : Chymotrypsin
- level : 0
- value : 7
- shown_as : CNBr
- level : 0
- value : 8
- name : Enzymes and Reagents
- type : full
- list_item :
- repeatable :
- list :
- base :
- base :
- name : mono
- ordering : 7
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : mono
- mandatory : false
- prompt : Use monoisotopic weights
- type : boolean
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- base :
- name : unfavoured
- ordering : 9
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Trypsin will not normally cut after ‘KR’ if they are followed by any of ‘KRIFLP’. Lys-C will not normally cut after ‘K’ if it is followed by ‘P’. Arg-C will not normally cut after ‘R’ if it is followed by ‘P’. V8-bicarb will not normally cut after ‘E’ if it is followed by any of ‘KREP’. V8-phosph will not normally cut after ‘DE’ if they are followed by ‘P’. Chymotrypsin will not normally cut after ‘FYWLM’ if they are followed by ‘P’. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones.
- default : false
- qualifier : unfavoured
- mandatory : false
- prompt : Allow unfavoured cuts
- type : boolean
- base :
- name : ragging
- ordering : 10
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Allows semi-specific and non-specific digestion. This option is particularly useful for generating lists of peptide sequences for protein identification using mass-spectrometry.
- default : false
- qualifier : ragging
- mandatory : false
- prompt : Allow ragging
- type : boolean
- choice_list :
- grouptype : zero_or_more
- separator : ,
- base :
- name : termini_1
- ordering : 12
- qualifier : 1
- default : true
- mandatory : false
- type : boolean
- prompt : none
- name : termini_2
- ordering : 13
- qualifier : 2
- default : false
- mandatory : false
- type : boolean
- prompt : nterm
- name : termini_3
- ordering : 14
- qualifier : 3
- default : false
- mandatory : false
- type : boolean
- prompt : cterm
- name : termini_4
- ordering : 15
- qualifier : 4
- default : false
- mandatory : false
- type : boolean
- prompt : nterm OR cterm
- base :
- base :
- name : overlap
- ordering : 18
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Used for partial digestion. Shows all cuts from favoured cut sites plus 1..3, 2..4, 3..5 etc but not (e.g.) 2..5. Overlaps are therefore fragments with exactly one potential cut site within it.
- default : false
- qualifier : overlap
- mandatory : false
- prompt : Show overlapping partials
- type : boolean
- base :
- name : allpartials
- ordering : 19
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : As for overlap but fragments containing more than one potential cut site are included.
- default : false
- qualifier : allpartials
- mandatory : false
- prompt : Show all partials
- type : boolean
- 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/digest.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : mono
- default : false
- mandatory : false
- type : boolean
- name : unfavoured
- default : false
- mandatory : false
- type : boolean
- name : ragging
- default : false
- mandatory : false
- type : boolean
- name : termini_1
- default : true
- mandatory : false
- type : boolean
- name : termini_2
- default : false
- mandatory : false
- type : boolean
- name : termini_3
- default : false
- mandatory : false
- type : boolean
- name : termini_4
- default : false
- mandatory : false
- type : boolean
- name : overlap
- default : false
- mandatory : false
- type : boolean
- name : allpartials
- default : false
- mandatory : false
- type : boolean
- analysis :
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