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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/edit.skipredundant
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/edit.skipredundant?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 : skipredundant
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove redundant sequences from an input set
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : skipredundant
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove redundant sequences from an input set
- 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 :
- standard :
- list :
- list_item :
- shown_as : Single threshold percentage sequence similarity
- level : 0
- value : 1
- shown_as : Outside a range of acceptable threshold percentage similarities
- level : 0
- value : 2
- name : Redundancy removal options
- type : full
- list_item :
- repeatable :
- list :
- base :
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : gapopen
- ordering : 11
- option :
- name : EDAM:0001397
- type : normal
- value : data Gap opening penalty
- 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
- 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.
- qualifier : gapopen
- mandatory : false
- prompt : Gap opening penalty
- type : float
- range :
- format : %f
- max : 10.0
- min : 0.0
- repeatable :
- base :
- name : gapextend
- ordering : 12
- option :
- name : EDAM:0001398
- type : normal
- value : data Gap extension penalty
- 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
- 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.
- qualifier : gapextend
- mandatory : false
- prompt : Gap extension penalty
- type : float
- base :
- name : feature
- ordering : 2
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Sequence feature information will be retained if this option is set.
- default : false
- qualifier : feature
- mandatory : false
- prompt : Use feature information
- type : boolean
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- repeatable :
- base :
- name : threshold
- ordering : 8
- option :
- name : EDAM:0002146
- type : normal
- value : data 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
- qualifier : threshold
- mandatory : false
- prompt : The percentage sequence identity redundancy threshold.
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : minthreshold
- ordering : 9
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- 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
- qualifier : minthreshold
- mandatory : false
- prompt : The % sequence identity redundancy threshold (lower limit).
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : maxthreshold
- ordering : 10
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- 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
- qualifier : maxthreshold
- mandatory : false
- prompt : The percentage sequence identity redundancy threshold (upper limit).
- type : float
- data :
- result :
- extension : keep
- iotype : output
- base :
- data :
- result :
- extension : redundant
- 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 :
- 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:0000220
- type : normal
- value : topic File handling
- name : EDAM:0000290
- type : normal
- value : operation Sequence redundancy removal
- name : EDAM:0000491
- type : normal
- value : operation Pairwise sequence alignment
- name : EDAM:0002121
- type : normal
- value : operation Sequence file handling
- 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 : edit
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/skipredundant.html
- event :
- action :
- id : _E_1
- parameter :
- 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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