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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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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/nucleic_translation.showseq
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/nucleic_translation.showseq?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) Displays sequences with features in pretty format
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 : showseq
- installation : Soaplab2 default installation
- type : Display, Nucleic Translation, Nucleic Restriction
- output :
- description : Displays sequences with features in pretty format
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : showseq
- installation : Soaplab2 default installation
- type : Display, Nucleic Translation, Nucleic Restriction
- output :
- description : Displays sequences with features in pretty format
- 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/showseq.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 : Things to display
- list_item :
- level : 0
- shown_as : Enter your own list of things to display
- value : 0
- level : 0
- shown_as : Sequence only
- value : 1
- level : 0
- shown_as : Default sequence with features
- value : 2
- level : 0
- shown_as : Pretty sequence
- value : 3
- level : 0
- shown_as : One frame translation
- value : 4
- level : 0
- shown_as : Three frame translations
- value : 5
- level : 0
- shown_as : Six frame translations
- value : 6
- level : 0
- shown_as : Restriction enzyme map
- value : 7
- level : 0
- shown_as : Baroque
- value : 8
- type : full
- repeatable :
- list :
- base :
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- choice_list :
- separator : ,
- grouptype : zero_or_more
- base :
- name : things_S
- default : true
- mandatory : false
- qualifier : S
- type : boolean
- prompt : Sequence
- ordering : 8
- name : things_B
- default : true
- mandatory : false
- qualifier : B
- type : boolean
- prompt : Blank line
- ordering : 9
- name : things_1
- default : false
- mandatory : false
- qualifier : 1
- type : boolean
- prompt : Frame1 translation
- ordering : 10
- name : things_2
- default : false
- mandatory : false
- qualifier : 2
- type : boolean
- prompt : Frame2 translation
- ordering : 11
- name : things_3
- default : false
- mandatory : false
- qualifier : 3
- type : boolean
- prompt : Frame3 translation
- ordering : 12
- name : things_-1
- default : false
- mandatory : false
- qualifier : -1
- type : boolean
- prompt : CompFrame1 translation
- ordering : 13
- name : things_-2
- default : false
- mandatory : false
- qualifier : -2
- type : boolean
- prompt : CompFrame2 translation
- ordering : 14
- name : things_-3
- default : false
- mandatory : false
- qualifier : -3
- type : boolean
- prompt : CompFrame3 translation
- ordering : 15
- name : things_T
- default : true
- mandatory : false
- qualifier : T
- type : boolean
- prompt : Ticks line
- ordering : 16
- name : things_N
- default : true
- mandatory : false
- qualifier : N
- type : boolean
- prompt : Number ticks line
- ordering : 17
- name : things_C
- default : false
- mandatory : false
- qualifier : C
- type : boolean
- prompt : Complement sequence
- ordering : 18
- name : things_F
- default : true
- mandatory : false
- qualifier : F
- type : boolean
- prompt : Features
- ordering : 19
- name : things_R
- default : false
- mandatory : false
- qualifier : R
- type : boolean
- prompt : Restriction enzyme cut sites in forward sense
- ordering : 20
- name : things_-R
- default : false
- mandatory : false
- qualifier : -R
- type : boolean
- prompt : Restriction enzyme cut sites in reverse sense
- ordering : 21
- name : things_A
- default : true
- mandatory : false
- qualifier : A
- type : boolean
- prompt : Annotation
- ordering : 22
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- 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 :
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : sensematch
- help : By default any feature type in the feature table is shown. You can set this to match any feature sense you wish to show. 0 – any sense, 1 – forward sense, -1 – reverse sense
- default : 0
- mandatory : false
- qualifier : sensematch
- prompt : Sense of feature to display
- type : long
- ordering : 35
- range :
- format : %f
- repeatable :
- base :
- name : minscore
- help : Minimum score of feature to display (see also maxscore)
- default : 0.0
- mandatory : false
- qualifier : minscore
- prompt : Minimum score of feature to display
- type : float
- ordering : 36
- range :
- format : %f
- repeatable :
- base :
- name : maxscore
- help : Maximum score of feature to display. If both minscore and maxscore are zero (the default), then any score is ignored
- default : 0.0
- mandatory : false
- qualifier : maxscore
- prompt : Maximum score of feature to display
- type : float
- ordering : 37
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : stricttags
- help : By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed.
- default : false
- mandatory : false
- qualifier : stricttags
- prompt : Only display the matching tags
- type : boolean
- ordering : 40
- 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 : 45
- 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 : 46
- 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 : 47
- 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 : 48
- 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 RE site only cuts
- type : boolean
- ordering : 49
- 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 RE cutters
- type : boolean
- ordering : 50
- 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 RE cutters
- type : boolean
- ordering : 51
- 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 RE matches
- type : boolean
- ordering : 52
- 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 : 53
- 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 : 54
- 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 use restriction enzymes with suppliers
- type : boolean
- ordering : 55
- 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 RE hits to one isoschizomer
- type : boolean
- ordering : 56
- 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 : 58
- base :
- name : threeletter
- default : false
- mandatory : false
- qualifier : threeletter
- prompt : Display protein sequences in three-letter code
- type : boolean
- ordering : 59
- base :
- name : number
- default : false
- mandatory : false
- qualifier : number
- prompt : Number the sequences
- type : boolean
- ordering : 60
- 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 : 61
- 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 : 62
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : margin
- default : 10
- mandatory : false
- qualifier : margin
- prompt : Margin around sequence for numbering
- type : long
- ordering : 63
- 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 : Show sequence ID
- type : boolean
- ordering : 64
- 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 : Show description
- type : boolean
- ordering : 65
- range :
- format : %d
- repeatable :
- base :
- name : offset
- default : 1
- mandatory : false
- qualifier : offset
- prompt : Offset to start numbering the sequence from
- type : long
- ordering : 66
- base :
- name : html
- default : false
- mandatory : false
- qualifier : html
- prompt : Use HTML formatting
- type : boolean
- ordering : 67
- data :
- option :
- input :
- name : things_S
- default : true
- mandatory : false
- type : boolean
- name : things_B
- default : true
- mandatory : false
- type : boolean
- name : things_1
- default : false
- mandatory : false
- type : boolean
- name : things_2
- default : false
- mandatory : false
- type : boolean
- name : things_3
- default : false
- mandatory : false
- type : boolean
- name : things_-1
- default : false
- mandatory : false
- type : boolean
- name : things_-2
- default : false
- mandatory : false
- type : boolean
- name : things_-3
- default : false
- mandatory : false
- type : boolean
- name : things_T
- default : true
- mandatory : false
- type : boolean
- name : things_N
- default : true
- mandatory : false
- type : boolean
- name : things_C
- default : false
- mandatory : false
- type : boolean
- name : things_F
- default : true
- mandatory : false
- type : boolean
- name : things_R
- default : false
- mandatory : false
- type : boolean
- name : things_-R
- default : false
- mandatory : false
- type : boolean
- name : things_A
- default : true
- mandatory : false
- type : boolean
- name : sensematch
- default : 0
- mandatory : false
- type : long
- name : minscore
- default : 0.0
- mandatory : false
- type : float
- name : maxscore
- default : 0.0
- mandatory : false
- type : float
- name : stricttags
- default : false
- mandatory : false
- type : boolean
- name : flatreformat
- default : false
- mandatory : false
- type : boolean
- name : mincuts
- default : 1
- mandatory : false
- type : long
- name : maxcuts
- default : 2000000000
- mandatory : false
- type : long
- name : sitelen
- default : 4
- 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 : limit
- 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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