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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/protein_2d_structure.garnier
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/protein_2d_structure.garnier?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/garnier.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Predicts protein secondary structure using GOR method
SoapLab Support(over 10 years ago)
Predicts protein secondary structure using GOR method
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 : garnier
- installation : Soaplab2 default installation
- type : Protein 2D Structure
- output :
- description : Predicts protein secondary structure using GOR method
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : garnier
- installation : Soaplab2 default installation
- type : Protein 2D Structure
- output :
- description : Predicts protein secondary structure using GOR method
- 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 : protein_2d_structure
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/garnier.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 :
- data :
- result :
- iotype : output
- base :
- range :
- format : %d
- max : 6
- min : 0
- repeatable :
- base :
- name : idc
- help : In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction. ‘idc’ is an index into a set of arrays, dharr[] and dsarr[], which provide ‘decision constants’ (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms. So, idc=0 says don’t use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used.
- default : 0
- option :
- name : scalemax
- type : style
- value : 6
- mandatory : false
- qualifier : idc
- prompt : Index decision constants parameter
- type : long
- ordering : 4
- data :
- option :
- input :
- name : idc
- default : 0
- mandatory : false
- type : long
- analysis :
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