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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_restriction.remap
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/nucleic_restriction.remap?wsdl(download last cached WSDL file)
Documentation URL(s): None Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Display restriction enzyme binding sites in a nucleotide sequence
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 : remap
- installation : Soaplab2 default installation
- type : Display, Nucleic Restriction, Nucleic Translation
- output :
- description : Display restriction enzyme binding sites in a nucleotide sequence
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : remap
- installation : Soaplab2 default installation
- type : Display, Nucleic Restriction, Nucleic Translation
- output :
- description : Display restriction enzyme binding sites in a nucleotide sequence
- 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 : display
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/remap.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 :
- repeatable :
- base :
- range :
- format : %d
- max : 20
- min : 2
- repeatable :
- base :
- name : sitelen
- help : This sets the minimum length of the restriction enzyme recognition site. Any enzymes with sites shorter than this will be ignored.
- default : 4
- option :
- name : scalemax
- type : style
- value : 20
- name : scalemin
- type : style
- value : 2
- mandatory : false
- qualifier : sitelen
- prompt : Minimum recognition site length
- type : long
- ordering : 7
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- max : 1000
- min : 1
- repeatable :
- base :
- name : mincuts
- 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
- option :
- name : scalemax
- type : style
- value : 1000
- name : scalemin
- type : style
- value : 1
- mandatory : false
- qualifier : mincuts
- prompt : Minimum cuts per RE
- type : long
- ordering : 9
- range :
- format : %d
- max : 2000000000
- min :
- repeatable :
- base :
- name : maxcuts
- 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
- option :
- name : calculated_hardmin
- type : normal
- value : ${mincuts}
- name : scalemax
- type : style
- value : 2000000000
- mandatory : false
- qualifier : maxcuts
- prompt : Maximum cuts per RE
- type : long
- ordering : 10
- base :
- name : single
- 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
- mandatory : false
- qualifier : single
- prompt : Force single site only cuts
- type : boolean
- ordering : 11
- base :
- name : blunt
- help : This allows those enzymes which cut at the same position on the forward and reverse strands to be considered.
- default : false
- mandatory : false
- qualifier : blunt
- prompt : Allow blunt end cutters
- type : boolean
- ordering : 12
- base :
- name : sticky
- help : This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered.
- default : false
- mandatory : false
- qualifier : sticky
- prompt : Allow sticky end cutters
- type : boolean
- ordering : 13
- base :
- name : ambiguity
- help : This allows those enzymes which have one or more ‘N’ ambiguity codes in their pattern to be considered
- default : false
- mandatory : false
- qualifier : ambiguity
- prompt : Allow ambiguous matches
- type : boolean
- ordering : 14
- base :
- name : plasmid
- help : If this is set then this allows searches for restriction enzyme recognition site and cut postions that span the end of the sequence to be considered.
- default : false
- mandatory : false
- qualifier : plasmid
- prompt : Allow circular DNA
- type : boolean
- ordering : 15
- base :
- name : methylation
- help : If this is set then RE recognition sites will not match methylated bases.
- default : false
- mandatory : false
- qualifier : methylation
- prompt : Use methylation data
- type : boolean
- ordering : 16
- base :
- name : commercial
- 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
- mandatory : false
- qualifier : commercial
- prompt : Only enzymes with suppliers
- type : boolean
- ordering : 17
- standard :
- list :
- name : Genetic codes
- list_item :
- level : 0
- shown_as : Standard
- value : 0
- level : 0
- shown_as : Standard (with alternative initiation codons)
- value : 1
- level : 0
- shown_as : Vertebrate Mitochondrial
- value : 2
- level : 0
- shown_as : Yeast Mitochondrial
- value : 3
- level : 0
- shown_as : Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
- value : 4
- level : 0
- shown_as : Invertebrate Mitochondrial
- value : 5
- level : 0
- shown_as : Ciliate Macronuclear and Dasycladacean
- value : 6
- level : 0
- shown_as : Echinoderm Mitochondrial
- value : 9
- level : 0
- shown_as : Euplotid Nuclear
- value : 10
- level : 0
- shown_as : Bacterial
- value : 11
- level : 0
- shown_as : Alternative Yeast Nuclear
- value : 12
- level : 0
- shown_as : Ascidian Mitochondrial
- value : 13
- level : 0
- shown_as : Flatworm Mitochondrial
- value : 14
- level : 0
- shown_as : Blepharisma Macronuclear
- value : 15
- level : 0
- shown_as : Chlorophycean Mitochondrial
- value : 16
- level : 0
- shown_as : Trematode Mitochondrial
- value : 21
- level : 0
- shown_as : Scenedesmus obliquus
- value : 22
- level : 0
- shown_as : Thraustochytrium Mitochondrial
- value : 23
- type : full
- repeatable :
- list :
- base :
- choice_list :
- separator : ,
- grouptype : zero_or_more
- base :
- name : frame_1
- default : false
- mandatory : false
- qualifier : 1
- type : boolean
- prompt : 1
- ordering : 20
- name : frame_2
- default : false
- mandatory : false
- qualifier : 2
- type : boolean
- prompt : 2
- ordering : 21
- name : frame_3
- default : false
- mandatory : false
- qualifier : 3
- type : boolean
- prompt : 3
- ordering : 22
- name : frame_F
- default : false
- mandatory : false
- qualifier : F
- type : boolean
- prompt : Forward three frames
- ordering : 23
- name : frame_-1
- default : false
- mandatory : false
- qualifier : -1
- type : boolean
- prompt : -1
- ordering : 24
- name : frame_-2
- default : false
- mandatory : false
- qualifier : -2
- type : boolean
- prompt : -2
- ordering : 25
- name : frame_-3
- default : false
- mandatory : false
- qualifier : -3
- type : boolean
- prompt : -3
- ordering : 26
- name : frame_R
- default : false
- mandatory : false
- qualifier : R
- type : boolean
- prompt : Reverse three frames
- ordering : 27
- name : frame_6
- default : true
- mandatory : false
- qualifier : 6
- type : boolean
- prompt : All six frames
- ordering : 28
- base :
- base :
- name : cutlist
- help : This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut.
- default : false
- mandatory : false
- qualifier : cutlist
- prompt : List the enzymes that cut
- type : boolean
- ordering : 32
- base :
- name : flatreformat
- help : This changes the output format to one where the recognition site is indicated by a row of ‘===’ characters and the cut site is pointed to by a ‘>’ character in the forward sense, or a ‘<‘ in the reverse sense strand.
- default : false
- mandatory : false
- qualifier : flatreformat
- prompt : Display RE sites in flat format
- type : boolean
- ordering : 33
- base :
- name : limit
- 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
- mandatory : false
- qualifier : limit
- prompt : Limits reports to one isoschizomer
- type : boolean
- ordering : 34
- base :
- name : translation
- help : This displays the 6-frame translations of the sequence in the output.
- default : false
- mandatory : false
- qualifier : translation
- prompt : Display translation
- type : boolean
- ordering : 35
- base :
- name : reverse
- help : This displays the cut sites and translation of the reverse sense.
- default : false
- mandatory : false
- qualifier : reverse
- prompt : Display cut sites and translation of reverse sense
- type : boolean
- ordering : 36
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : orfminsize
- help : This sets the minimum size of Open Reading Frames (ORFs) to display in the translations. All other translation regions are masked by changing the amino acids to ‘-‘ characters.
- default : 0
- mandatory : false
- qualifier : orfminsize
- prompt : Minimum size of ORFs
- type : long
- ordering : 37
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : threeletter
- default : false
- mandatory : false
- qualifier : threeletter
- prompt : Display protein sequences in three-letter code
- type : boolean
- ordering : 40
- base :
- name : number
- default : false
- mandatory : false
- qualifier : number
- prompt : Number the sequences
- type : boolean
- ordering : 41
- range :
- format : %d
- min : 1
- repeatable :
- base :
- name : width
- default : 60
- option :
- name : scalemin
- type : style
- value : 1
- mandatory : false
- qualifier : width
- prompt : Width of sequence to display
- type : long
- ordering : 42
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : length
- default : 0
- mandatory : false
- qualifier : length
- prompt : Line length of page (0 for indefinite)
- type : long
- ordering : 43
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : margin
- default : 10
- mandatory : false
- qualifier : margin
- prompt : Margin around sequence for numbering
- type : long
- ordering : 44
- base :
- name : name
- help : Set this to be false if you do not wish to display the ID name of the sequence
- default : false
- mandatory : false
- qualifier : name
- prompt : Display sequence ID
- type : boolean
- ordering : 45
- base :
- name : description
- help : Set this to be false if you do not wish to display the description of the sequence
- default : false
- mandatory : false
- qualifier : description
- prompt : Display description
- type : boolean
- ordering : 46
- range :
- format : %d
- repeatable :
- base :
- name : offset
- default : 1
- mandatory : false
- qualifier : offset
- prompt : Offset to start numbering the sequence from
- type : long
- ordering : 47
- base :
- name : html
- default : false
- mandatory : false
- qualifier : html
- prompt : Use HTML formatting
- type : boolean
- ordering : 48
- data :
- option :
- input :
- name : sitelen
- default : 4
- mandatory : false
- type : long
- name : mincuts
- default : 1
- mandatory : false
- type : long
- name : maxcuts
- default : 2000000000
- mandatory : false
- type : long
- 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 : frame_1
- default : false
- mandatory : false
- type : boolean
- name : frame_2
- default : false
- mandatory : false
- type : boolean
- name : frame_3
- default : false
- mandatory : false
- type : boolean
- name : frame_F
- default : false
- mandatory : false
- type : boolean
- name : frame_-1
- default : false
- mandatory : false
- type : boolean
- name : frame_-2
- default : false
- mandatory : false
- type : boolean
- name : frame_-3
- default : false
- mandatory : false
- type : boolean
- name : frame_R
- default : false
- mandatory : false
- type : boolean
- name : frame_6
- default : true
- mandatory : false
- type : boolean
- name : cutlist
- default : false
- mandatory : false
- type : boolean
- name : flatreformat
- default : false
- mandatory : false
- type : boolean
- name : limit
- default : false
- mandatory : false
- type : boolean
- name : translation
- default : false
- mandatory : false
- type : boolean
- name : reverse
- default : false
- mandatory : false
- type : boolean
- name : orfminsize
- default : 0
- mandatory : false
- type : long
- name : threeletter
- default : false
- mandatory : false
- type : boolean
- name : number
- default : false
- mandatory : false
- type : boolean
- name : width
- default : 60
- mandatory : false
- type : long
- name : length
- default : 0
- mandatory : false
- type : long
- name : margin
- default : 10
- mandatory : false
- type : long
- name : name
- default : false
- mandatory : false
- type : boolean
- name : description
- default : false
- mandatory : false
- type : boolean
- name : offset
- default : 1
- mandatory : false
- type : long
- name : html
- default : false
- mandatory : false
- type : boolean
- analysis :
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