This looks like a Soaplab service. Click here for more info and guidance on how to use this service )
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.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
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:
SoapLab Support (over 11 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/protein_motifs.digest
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/protein_motifs.digest?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/digest.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Reports on protein proteolytic enzyme or reagent cleavage sites
SoapLab Support(over 10 years ago)
Reports on protein proteolytic enzyme or reagent cleavage sites
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 : digest
- installation : Soaplab2 default installation
- type : Protein Motifs
- output :
- description : Reports on protein proteolytic enzyme or reagent cleavage sites
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : digest
- installation : Soaplab2 default installation
- type : Protein Motifs
- output :
- description : Reports on protein proteolytic enzyme or reagent cleavage sites
- 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 : protein_motifs
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/digest.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 :
- standard :
- list :
- name : Enzymes and Reagents
- list_item :
- level : 0
- shown_as : Trypsin
- value : 1
- level : 0
- shown_as : Lys-C
- value : 2
- level : 0
- shown_as : Arg-C
- value : 3
- level : 0
- shown_as : Asp-N
- value : 4
- level : 0
- shown_as : V8-bicarb
- value : 5
- level : 0
- shown_as : V8-phosph
- value : 6
- level : 0
- shown_as : Chymotrypsin
- value : 7
- level : 0
- shown_as : CNBr
- value : 8
- type : full
- repeatable :
- list :
- base :
- base :
- name : mono
- default : false
- mandatory : false
- qualifier : mono
- prompt : Use monoisotopic weights
- type : boolean
- ordering : 7
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- base :
- name : unfavoured
- 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
- mandatory : false
- qualifier : unfavoured
- prompt : Allow unfavoured cuts
- type : boolean
- ordering : 9
- base :
- name : ragging
- 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
- mandatory : false
- qualifier : ragging
- prompt : Allow ragging
- type : boolean
- ordering : 10
- choice_list :
- separator : ,
- grouptype : zero_or_more
- base :
- name : termini_1
- default : true
- mandatory : false
- qualifier : 1
- type : boolean
- prompt : none
- ordering : 12
- name : termini_2
- default : false
- mandatory : false
- qualifier : 2
- type : boolean
- prompt : nterm
- ordering : 13
- name : termini_3
- default : false
- mandatory : false
- qualifier : 3
- type : boolean
- prompt : cterm
- ordering : 14
- name : termini_4
- default : false
- mandatory : false
- qualifier : 4
- type : boolean
- prompt : nterm OR cterm
- ordering : 15
- base :
- base :
- name : overlap
- 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
- mandatory : false
- qualifier : overlap
- prompt : Show overlapping partials
- type : boolean
- ordering : 18
- base :
- name : allpartials
- help : As for overlap but fragments containing more than one potential cut site are included.
- default : false
- mandatory : false
- qualifier : allpartials
- prompt : Show all partials
- type : boolean
- ordering : 19
- data :
- option :
- 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 :
License(s): No info yet Login to add license info Cost: No info yet Login to add cost info Usage conditions: No info yet Login to add usage conditions info Contact info: No info yet Login to add contact info How to cite this service: No info yet Login to add how to cite info Publications about this service: for this service (this can be in a common citation format like Bibtex, MLA or APA, a DOI, a URL, etc.) No info yet Login to add publications info Citations of this service: No info yet Login to add citations info Example workflows using this service: See all workflows on myExperiment that use this service Login to add workflows info