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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_translation.transeq
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/nucleic_translation.transeq?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 : transeq
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Translation
- description : Translate nucleic acid sequences
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : transeq
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Nucleic Translation
- description : Translate nucleic acid sequences
- 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 :
- choice_list :
- grouptype : zero_or_more
- separator : ,
- base :
- name : frame_1
- ordering : 5
- qualifier : 1
- default : true
- mandatory : false
- type : boolean
- prompt : 1
- name : frame_2
- ordering : 6
- qualifier : 2
- default : false
- mandatory : false
- type : boolean
- prompt : 2
- name : frame_3
- ordering : 7
- qualifier : 3
- default : false
- mandatory : false
- type : boolean
- prompt : 3
- name : frame_F
- ordering : 8
- qualifier : F
- default : false
- mandatory : false
- type : boolean
- prompt : Forward three frames
- name : frame_-1
- ordering : 9
- qualifier : -1
- default : false
- mandatory : false
- type : boolean
- prompt : -1
- name : frame_-2
- ordering : 10
- qualifier : -2
- default : false
- mandatory : false
- type : boolean
- prompt : -2
- name : frame_-3
- ordering : 11
- qualifier : -3
- default : false
- mandatory : false
- type : boolean
- prompt : -3
- name : frame_R
- ordering : 12
- qualifier : R
- default : false
- mandatory : false
- type : boolean
- prompt : Reverse three frames
- name : frame_6
- ordering : 13
- qualifier : 6
- default : false
- mandatory : false
- type : boolean
- prompt : All six frames
- base :
- standard :
- list :
- list_item :
- shown_as : Standard
- level : 0
- value : 0
- shown_as : Standard (with alternative initiation codons)
- level : 0
- value : 1
- shown_as : Vertebrate Mitochondrial
- level : 0
- value : 2
- shown_as : Yeast Mitochondrial
- level : 0
- value : 3
- shown_as : Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma
- level : 0
- value : 4
- shown_as : Invertebrate Mitochondrial
- level : 0
- value : 5
- shown_as : Ciliate Macronuclear and Dasycladacean
- level : 0
- value : 6
- shown_as : Echinoderm Mitochondrial
- level : 0
- value : 9
- shown_as : Euplotid Nuclear
- level : 0
- value : 10
- shown_as : Bacterial
- level : 0
- value : 11
- shown_as : Alternative Yeast Nuclear
- level : 0
- value : 12
- shown_as : Ascidian Mitochondrial
- level : 0
- value : 13
- shown_as : Flatworm Mitochondrial
- level : 0
- value : 14
- shown_as : Blepharisma Macronuclear
- level : 0
- value : 15
- shown_as : Chlorophycean Mitochondrial
- level : 0
- value : 16
- shown_as : Trematode Mitochondrial
- level : 0
- value : 21
- shown_as : Scenedesmus obliquus
- level : 0
- value : 22
- shown_as : Thraustochytrium Mitochondrial
- level : 0
- value : 23
- name : Genetic codes
- type : full
- list_item :
- repeatable :
- list :
- base :
- standard :
- repeatable :
- base :
- base :
- name : trim
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This removes all ‘X’ and ‘*’ characters from the right end of the translation. The trimming process starts at the end and continues until the next character is not a ‘X’ or a ‘*’
- default : false
- qualifier : trim
- mandatory : false
- prompt : Trim trailing X’s and *’s
- type : boolean
- base :
- name : clean
- ordering : 17
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : This changes all STOP codon positions from the ‘*’ character to ‘X’ (an unknown residue). This is useful because some programs will not accept protein sequences with ‘*’ characters in them.
- default : false
- qualifier : clean
- mandatory : false
- prompt : Change all *’s to X’s
- type : boolean
- base :
- name : alternative
- ordering : 20
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : The default definition of frame ‘-1’ is the reverse-complement of the set of codons used in frame 1. (Frame -2 is the set of codons used by frame 2, similarly frames -3 and 3). This is a common standard, used by the Staden package and other programs. If you prefer to define frame ‘-1’ as using the set of codons starting with the last codon of the sequence, then set this to be true.
- default : false
- qualifier : alternative
- mandatory : false
- prompt : Define frame ‘-1’ as starting in the last codon
- type : boolean
- data :
- result :
- extension : pep
- iotype : output
- base :
- standard :
- list :
- list_item :
- level : 0
- value : acedb
- level : 0
- value : asn1
- level : 0
- value : bam
- level : 0
- value : clustal
- level : 0
- value : codata
- level : 0
- value : das
- level : 0
- value : dasdna
- level : 0
- value : embl
- level : 0
- value : experiment
- level : 0
- value : fasta
- 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 : jackknifer
- level : 0
- value : jackknifernon
- level : 0
- value : mase
- level : 0
- value : mega
- level : 0
- value : meganon
- level : 0
- value : msf
- level : 0
- value : nbrf
- level : 0
- value : ncbi
- level : 0
- value : nexus
- level : 0
- value : nexusnon
- level : 0
- value : phylip
- level : 0
- value : phylipnon
- level : 0
- value : pir
- level : 0
- value : raw
- level : 0
- value : refseq
- level : 0
- value : refseqp
- level : 0
- value : sam
- level : 0
- value : selex
- level : 0
- value : staden
- level : 0
- value : strider
- level : 0
- value : swiss
- level : 0
- value : text
- level : 0
- value : treecon
- type : full
- list_item :
- repeatable :
- list :
- base :
- data :
- option :
- name : EDAM:0000108
- type : normal
- value : topic Transcription and translation
- name : EDAM:0000371
- type : normal
- value : operation DNA translation
- 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_translation
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/transeq.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : frame_1
- default : true
- 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 : false
- mandatory : false
- type : boolean
- name : trim
- default : false
- mandatory : false
- type : boolean
- name : clean
- default : false
- mandatory : false
- type : boolean
- name : alternative
- default : false
- mandatory : false
- type : boolean
- analysis :
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