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:
Mike Mayer (over 9 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/nucleic_restriction.restrict
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/nucleic_restriction.restrict?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 : restrict
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Restriction
- description : Report restriction enzyme cleavage sites in a nucleotide sequence
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : restrict
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Restriction
- description : Report restriction enzyme cleavage sites in a nucleotide sequence
- 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 : 20
- min : 2
- repeatable :
- base :
- name : sitelen
- ordering : 7
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- name : scalemax
- type : style
- value : 20
- name : scalemin
- type : style
- value : 2
- help : This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored.
- default : 4
- qualifier : sitelen
- mandatory : false
- prompt : Minimum recognition site length
- type : long
- standard :
- repeatable :
- base :
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- max : 1000
- min : 1
- repeatable :
- base :
- name : min
- ordering : 10
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : scalemax
- type : style
- value : 1000
- name : scalemin
- type : style
- value : 1
- help : This sets the minimum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut fewer times than this will be ignored.
- default : 1
- qualifier : min
- mandatory : false
- prompt : Minimum cuts per RE
- type : long
- range :
- format : %d
- min :
- repeatable :
- base :
- name : max
- ordering : 11
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : calculated_hardmin
- type : normal
- value : ${min}
- help : This sets the maximum number of cuts for any restriction enzyme that will be considered. Any enzymes that cut more times than this will be ignored.
- default : 2000000000
- qualifier : max
- mandatory : false
- prompt : Maximum cuts per RE
- type : long
- base :
- name : solofragment
- ordering : 12
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This gives the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own. Results are added to the tail section of the report.
- default : false
- qualifier : solofragment
- mandatory : false
- prompt : List individual enzymes with their fragments
- type : boolean
- base :
- name : single
- ordering : 13
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1. Any other value you may have set them to will be ignored.
- default : false
- qualifier : single
- mandatory : false
- prompt : Force single site only cuts
- type : boolean
- base :
- name : blunt
- ordering : 14
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This allows those enzymes which cut at the same position on the forward and reverse strands to be considered.
- default : false
- qualifier : blunt
- mandatory : false
- prompt : Allow blunt end cutters
- type : boolean
- base :
- name : sticky
- ordering : 15
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered.
- default : false
- qualifier : sticky
- mandatory : false
- prompt : Allow sticky end cutters
- type : boolean
- base :
- name : ambiguity
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This allows those enzymes which have one or more ‘N’ ambiguity codes in their pattern to be considered
- default : false
- qualifier : ambiguity
- mandatory : false
- prompt : Allow ambiguous matches
- type : boolean
- base :
- name : plasmid
- ordering : 17
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered.
- default : false
- qualifier : plasmid
- mandatory : false
- prompt : Allow circular DNA
- type : boolean
- base :
- name : methylation
- ordering : 18
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set then RE recognition sites will not match methylated bases.
- default : false
- qualifier : methylation
- mandatory : false
- prompt : Use methylation data
- type : boolean
- base :
- name : commercial
- ordering : 19
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set, then only those enzymes with a commercial supplier will be searched for. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through ‘all’ the enzymes in the REBASE database. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier.
- default : false
- qualifier : commercial
- mandatory : false
- prompt : Only enzymes with suppliers
- type : boolean
- base :
- name : limit
- ordering : 22
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This limits the reporting of enzymes to just one enzyme from each group of isoschizomers. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file ’embossre.equ’, which is created by the program ‘rebaseextract’. If you prefer different prototypes to be used, make a copy of embossre.equ in your home directory and edit it. If this value is set to be false then all of the input enzymes will be reported. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching ‘all’ of them.
- default : false
- qualifier : limit
- mandatory : false
- prompt : Limits reports to one isoschizomer
- type : boolean
- base :
- name : alphabetic
- ordering : 23
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : alphabetic
- mandatory : false
- prompt : Sort output alphabetically
- type : boolean
- base :
- name : fragments
- ordering : 24
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together. Results are added to the tail section of the report.
- default : false
- qualifier : fragments
- mandatory : false
- prompt : Show fragment lengths
- type : boolean
- base :
- name : name
- ordering : 25
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : name
- mandatory : false
- prompt : Show sequence name
- type : boolean
- data :
- option :
- name : EDAM:0000100
- type : normal
- value : topic Nucleic acid restriction
- name : EDAM:0000431
- type : normal
- value : operation Restriction site identification
- 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_restriction
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/restrict.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : sitelen
- default : 4
- mandatory : false
- type : long
- name : min
- default : 1
- mandatory : false
- type : long
- name : max
- default : 2000000000
- mandatory : false
- type : long
- name : solofragment
- default : false
- mandatory : false
- type : boolean
- name : single
- default : false
- mandatory : false
- type : boolean
- name : blunt
- default : false
- mandatory : false
- type : boolean
- name : sticky
- default : false
- mandatory : false
- type : boolean
- name : ambiguity
- default : false
- mandatory : false
- type : boolean
- name : plasmid
- default : false
- mandatory : false
- type : boolean
- name : methylation
- default : false
- mandatory : false
- type : boolean
- name : commercial
- default : false
- mandatory : false
- type : boolean
- name : limit
- default : false
- mandatory : false
- type : boolean
- name : alphabetic
- default : false
- mandatory : false
- type : boolean
- name : fragments
- default : false
- mandatory : false
- type : boolean
- name : name
- 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