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Further documentation on Soaplab services is available:
- Soaplab overview
- Soaplab client guide page
- EBI Soaplab server documentation
- Soaplab 2
- Sourceforge site for EMBOSS Soaplab services
Provider:
European Bioinformatics Institute (EBI)
Location:
United Kingdom
Submitter / Source:
uludag (over 2 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/protein_3d_structure.sigscan
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/protein_3d_structure.sigscan?wsdl(download last cached WSDL file)
Documentation URL(s): uludag (about 1 year ago)http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/sigscan.html
Login to add a documentation URL Description(s): from provider’s description doc (10 months ago) Generates hits (DHF file) from a signature search
Franck Tanoh (about 1 year ago)sigscan scans a signature such as that generated by the EMBOSS application siggen against a protein sequence database and generates files of scored hits and corresponding alignments. An (optionally grouped) scop families file can be provided in which case a classification of hits is provided in the signature hits output file
uludag (about 1 year ago)Generate hits (DHF file) from a signature search.
Login to add a description Details (from Soaplab server): from Soaplab server(10 months ago)
- ds_lsr_analysis :
- analysis :
- name : sigscan
- output :
- version : 6.1.0
- type : Protein 3D Structure
- installation : Soaplab2 default installation
- description : Generates hits (DHF file) from a signature search
- input :
- analysis_extension :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : sigscan
- output :
- version : 6.1.0
- type : Protein 3D Structure
- installation : Soaplab2 default installation
- description : Generates hits (DHF file) from a signature search
- input :
- name : gapo
- default : 10
- mandatory : false
- type : float
- name : gape
- default : 0.5
- mandatory : false
- type : float
- name : nhits
- default : 100
- mandatory : false
- type : long
- analysis_extension :
- 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 :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- max : 100.
- min : 1.
- repeatable :
- base :
- ordering : 6
- name : gapo
- option :
- name : scalemax
- value : 100.
- type : style
- name : scalemin
- value : 1.
- type : style
- help : This option specifies the gap insertion penalty. The gap insertion 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 EDNAMAT matrix for nucleotide sequences.
- qualifier : gapo
- default : 10
- mandatory : false
- type : float
- prompt : Gap insertion penalty
- range :
- format : %f
- max : 10.
- min : 0.0
- repeatable :
- base :
- ordering : 7
- name : gape
- option :
- name : scalemax
- value : 10.
- type : style
- name : scalemin
- value : 0.0
- type : style
- help : This option specifies the gap extension penalty. 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.
- qualifier : gape
- default : 0.5
- mandatory : false
- type : float
- prompt : Gap extension penalty
- standard :
- list :
- list_item :
- shown_as : Align anywhere and allow only complete signature-sequence fit
- level : 0
- value : 1
- shown_as : Align anywhere and allow partial signature-sequence fit
- level : 0
- value : 2
- shown_as : Use empirical gaps only
- level : 0
- value : 3
- name : N-terminal matching options
- type : full
- list_item :
- repeatable :
- list :
- base :
- range :
- format : %d
- repeatable :
- base :
- ordering : 9
- name : nhits
- help : This option specifies the maximum number of hits to output.
- qualifier : nhits
- default : 100
- mandatory : false
- type : long
- prompt : Max. number of hits to output
- data :
- result :
- iotype : output
- base :
- data :
- result :
- iotype : output
- base :
- data :
- option :
- name : emboss
- value : true
- type : normal
- name : installation
- value : Soaplab2 default installation
- type : normal
- name : version
- value : 6.1.0
- type : normal
- app_info :
- category : protein_3d_structure
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/sigscan.html
- event :
- action :
- id : _E_1
- parameter :
- analysis :
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