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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.skipredundant
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/edit.skipredundant?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/skipredundant.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Remove redundant sequences from an input set
SoapLab Support(over 10 years ago)
Remove redundant sequences from an input set
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 : skipredundant
- installation : Soaplab2 default installation
- type : Edit
- output :
- description : Remove redundant sequences from an input set
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : skipredundant
- installation : Soaplab2 default installation
- type : Edit
- output :
- description : Remove redundant sequences from an input set
- 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/skipredundant.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 : Redundancy removal options
- list_item :
- level : 0
- shown_as : Single threshold percentage sequence similarity
- value : 1
- level : 0
- shown_as : Outside a range of acceptable threshold percentage similarities
- value : 2
- type : full
- repeatable :
- list :
- base :
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : gapopen
- help : The gap open penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences.
- option :
- name : calculated_default
- type : normal
- value : ${acdprotein}? 10.0 : 10.0
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : gapopen
- prompt : Gap opening penalty
- type : float
- ordering : 11
- range :
- format : %f
- max : 10.0
- min : 0.0
- repeatable :
- base :
- name : gapextend
- help : The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.
- option :
- name : calculated_default
- type : normal
- value : ${acdprotein}? 0.5 : 0.5
- name : scalemax
- type : style
- value : 10.0
- name : scalemin
- type : style
- value : 0.0
- mandatory : false
- qualifier : gapextend
- prompt : Gap extension penalty
- type : float
- ordering : 12
- base :
- name : feature
- help : Sequence feature information will be retained if this option is set.
- default : false
- mandatory : false
- qualifier : feature
- prompt : Use feature information
- type : boolean
- ordering : 2
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- repeatable :
- base :
- name : threshold
- help : This option specifies the percentage sequence identity redundancy threshold. The percentage sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded.
- default : 95.0
- mandatory : false
- qualifier : threshold
- prompt : The percentage sequence identity redundancy threshold.
- type : float
- ordering : 8
- range :
- format : %f
- repeatable :
- base :
- name : minthreshold
- help : This option specifies the percentage sequence identity redundancy threshold (lower limit). The percentage sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded.
- default : 30.0
- mandatory : false
- qualifier : minthreshold
- prompt : The % sequence identity redundancy threshold (lower limit).
- type : float
- ordering : 9
- range :
- format : %f
- repeatable :
- base :
- name : maxthreshold
- help : This option specifies the percentage sequence identity redundancy threshold (upper limit). The percentage sequence identity redundancy threshold determines the redundancy calculation. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded.
- default : 90.0
- mandatory : false
- qualifier : maxthreshold
- prompt : The percentage sequence identity redundancy threshold (upper limit).
- type : float
- ordering : 10
- data :
- result :
- extension : keep
- iotype : output
- base :
- data :
- result :
- extension : redundant
- 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 :
- 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 : feature
- default : false
- mandatory : false
- type : boolean
- name : threshold
- default : 95.0
- mandatory : false
- type : float
- name : minthreshold
- default : 30.0
- mandatory : false
- type : float
- name : maxthreshold
- default : 90.0
- mandatory : false
- type : float
- analysis :
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