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- Soaplab overview
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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/edit.trimseq
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/edit.trimseq?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/trimseq.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Remove unwanted characters from start and end of sequence(s)
SoapLab Support(over 10 years ago)
Remove unwanted characters from start and end of sequence(s)
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 : trimseq
- installation : Soaplab2 default installation
- type : Edit
- output :
- description : Remove unwanted characters from start and end of sequence(s)
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : trimseq
- installation : Soaplab2 default installation
- type : Edit
- output :
- description : Remove unwanted characters from start and end of sequence(s)
- 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 : edit
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/trimseq.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 :
- range :
- format : %d
- repeatable :
- base :
- name : window
- help : This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage.
- default : 1
- mandatory : false
- qualifier : window
- prompt : Window size
- type : long
- ordering : 4
- range :
- format : %f
- repeatable :
- base :
- name : percent
- help : This is the threshold of the percentage ambiguity in the window required in order to trim a sequence.
- default : 100.0
- mandatory : false
- qualifier : percent
- prompt : Percent threshold of ambiguity in window
- type : float
- ordering : 5
- base :
- name : strict
- help : In nucleic sequences, trim off not only N’s and X’s, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X’s but also B and Z.
- default : false
- mandatory : false
- qualifier : strict
- prompt : Trim off all ambiguity codes, not just N or X
- type : boolean
- ordering : 6
- base :
- name : star
- help : In protein sequences, trim off not only X’s, but also the *’s
- default : false
- mandatory : false
- qualifier : star
- prompt : Trim off asterisks
- type : boolean
- ordering : 7
- base :
- name : left
- default : false
- mandatory : false
- qualifier : left
- prompt : Trim at the start
- type : boolean
- ordering : 10
- base :
- name : right
- default : false
- mandatory : false
- qualifier : right
- prompt : Trim at the end
- type : boolean
- ordering : 11
- data :
- result :
- iotype : output
- base :
- standard :
- 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 :
- repeatable :
- list :
- base :
- data :
- option :
- input :
- name : window
- default : 1
- mandatory : false
- type : long
- name : percent
- default : 100.0
- mandatory : false
- type : float
- name : strict
- default : false
- mandatory : false
- type : boolean
- name : star
- default : false
- mandatory : false
- type : boolean
- name : left
- default : false
- mandatory : false
- type : boolean
- name : right
- default : false
- mandatory : false
- type : boolean
- analysis :
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