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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
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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/feature_tables.extractfeat
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/feature_tables.extractfeat?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) Extract features from 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 : extractfeat
- installation : Soaplab2 default installation
- type : Edit, Feature tables
- output :
- description : Extract features from sequence(s)
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : extractfeat
- installation : Soaplab2 default installation
- type : Edit, Feature tables
- output :
- description : Extract features from 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/extractfeat.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 : before
- help : If this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature. So a value of ’10’ will start the extraction 10 bases/residues before the start of the sequence, and a value of ‘-10’ will start the extraction 10 bases/residues before the end of the feature. The output sequence will be padded with ‘N’ or ‘X’ characters if the sequence starts after the required start of the extraction.
- default : 0
- mandatory : false
- qualifier : before
- prompt : Amount of sequence before feature to extract
- type : long
- ordering : 4
- range :
- format : %d
- repeatable :
- base :
- name : after
- help : If this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature. So a value of ’10’ will end the extraction 10 bases/residues after the end of the sequence, and a value of ‘-10’ will end the extraction 10 bases/residues after the start of the feature. The output sequence will be padded with ‘N’ or ‘X’ characters if the sequence ends before the required end of the extraction.
- default : 0
- mandatory : false
- qualifier : after
- prompt : Amount of sequence after feature to extract
- type : long
- ordering : 5
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : sense
- help : By default any feature type in the feature table is extracted. You can set this to match any feature sense you wish. 0 – any sense, 1 – forward sense, -1 – reverse sense
- default : 0
- mandatory : false
- qualifier : sense
- prompt : Sense of feature to extract
- type : long
- ordering : 8
- range :
- format : %f
- repeatable :
- base :
- name : minscore
- help : Minimum score of feature to extract (see also maxscore)
- default : 0.0
- mandatory : false
- qualifier : minscore
- prompt : Minimum score of feature to extract
- type : float
- ordering : 9
- range :
- format : %f
- repeatable :
- base :
- name : maxscore
- help : Maximum score of feature to extract. 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 extract
- type : float
- ordering : 10
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- base :
- name : join
- help : Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together. There may be other forms of ‘joined’ sequence, depending on the feature table. If this option is set TRUE, then any group of these features will be output as a single sequence. If the ‘before’ and ‘after’ qualifiers have been set, then only the sequence before the first feature and after the last feature are added.
- default : false
- mandatory : false
- qualifier : join
- prompt : Output introns etc. as one sequence
- type : boolean
- ordering : 15
- base :
- name : featinname
- help : To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name. If you set this to be TRUE then the name is added to the ID name of the output sequence.
- default : false
- mandatory : false
- qualifier : featinname
- prompt : Append type of feature to output sequence name
- type : boolean
- ordering : 16
- standard :
- repeatable :
- base :
- 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 : before
- default : 0
- mandatory : false
- type : long
- name : after
- default : 0
- mandatory : false
- type : long
- name : sense
- 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 : join
- default : false
- mandatory : false
- type : boolean
- name : featinname
- default : false
- mandatory : false
- type : boolean
- analysis :
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