This looks like a Soaplab service. Click here for more info and guidance on how to use this service )
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.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
More information on Soaplab clients is available here.
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 (EMBL-EBI)
Location:
United Kingdom
Submitter/Source:
SoapLab Support (almost 12 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/alignment_global.est2genome
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/alignment_global.est2genome?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/est2genome.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Align EST sequences to genomic DNA sequence
SoapLab Support(over 10 years ago)
Align EST sequences to genomic DNA sequence
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 : est2genome
- installation : Soaplab2 default installation
- type : Alignment Global
- output :
- description : Align EST sequences to genomic DNA sequence
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : est2genome
- installation : Soaplab2 default installation
- type : Alignment Global
- output :
- description : Align EST sequences to genomic DNA sequence
- 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 : alignment_global
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/est2genome.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 :
- 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
- repeatable :
- base :
- name : match
- default : 1
- mandatory : false
- qualifier : match
- prompt : Score for matching two bases
- type : long
- ordering : 5
- range :
- format : %d
- repeatable :
- base :
- name : mismatch
- default : 1
- mandatory : false
- qualifier : mismatch
- prompt : Cost for mismatching two bases
- type : long
- ordering : 6
- range :
- format : %d
- repeatable :
- base :
- name : gappenalty
- help : Cost for deleting a single base in either sequence, excluding introns
- default : 2
- mandatory : false
- qualifier : gappenalty
- prompt : Gap penalty
- type : long
- ordering : 7
- range :
- format : %d
- repeatable :
- base :
- name : intronpenalty
- help : Cost for an intron, independent of length.
- default : 40
- mandatory : false
- qualifier : intronpenalty
- prompt : Intron penalty
- type : long
- ordering : 8
- range :
- format : %d
- repeatable :
- base :
- name : splicepenalty
- help : Cost for an intron, independent of length and starting/ending on donor-acceptor sites
- default : 20
- mandatory : false
- qualifier : splicepenalty
- prompt : Splice site penalty
- type : long
- ordering : 9
- range :
- format : %d
- repeatable :
- base :
- name : minscore
- help : Exclude alignments with scores below this threshold score.
- default : 30
- mandatory : false
- qualifier : minscore
- prompt : Minimum accepted score
- type : long
- ordering : 10
- base :
- name : reverse
- help : Reverse the orientation of the EST sequence
- default : false
- mandatory : false
- qualifier : reverse
- prompt : Reverse orientation
- type : boolean
- ordering : 13
- base :
- name : usesplice
- help : Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false.
- default : false
- mandatory : false
- qualifier : usesplice
- prompt : Use donor and acceptor splice sites
- type : boolean
- ordering : 14
- choice_list :
- separator : ,
- grouptype : zero_or_more
- base :
- name : mode_both
- default : true
- mandatory : false
- qualifier : both
- type : boolean
- prompt : Both strands
- ordering : 16
- name : mode_forward
- default : false
- mandatory : false
- qualifier : forward
- type : boolean
- prompt : Forward strand only
- ordering : 17
- name : mode_reverse
- default : false
- mandatory : false
- qualifier : reverse
- type : boolean
- prompt : Reverse strand only
- ordering : 18
- base :
- base :
- name : best
- help : You can print out all comparisons instead of just the best one by setting this to be false.
- default : false
- mandatory : false
- qualifier : best
- prompt : Print out only best alignment
- type : boolean
- ordering : 19
- range :
- format : %f
- repeatable :
- base :
- name : space
- help : For linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine’s physical RAM)
- default : 10.0
- mandatory : false
- qualifier : space
- prompt : Space threshold (in megabytes)
- type : float
- ordering : 20
- range :
- format : %d
- repeatable :
- base :
- name : shuffle
- mandatory : false
- qualifier : shuffle
- prompt : Shuffle
- type : long
- ordering : 21
- range :
- format : %d
- repeatable :
- base :
- name : seed
- default : 20825
- mandatory : false
- qualifier : seed
- prompt : Random number seed
- type : long
- ordering : 22
- base :
- name : align
- help : Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown).
- default : false
- mandatory : false
- qualifier : align
- prompt : Show the alignment
- type : boolean
- ordering : 26
- range :
- format : %d
- repeatable :
- base :
- name : width
- default : 50
- mandatory : false
- qualifier : width
- prompt : Alignment width
- type : long
- ordering : 27
- data :
- option :
- input :
- name : match
- default : 1
- mandatory : false
- type : long
- name : mismatch
- default : 1
- mandatory : false
- type : long
- name : gappenalty
- default : 2
- mandatory : false
- type : long
- name : intronpenalty
- default : 40
- mandatory : false
- type : long
- name : splicepenalty
- default : 20
- mandatory : false
- type : long
- name : minscore
- default : 30
- mandatory : false
- type : long
- name : reverse
- default : false
- mandatory : false
- type : boolean
- name : usesplice
- default : false
- mandatory : false
- type : boolean
- name : mode_both
- default : true
- mandatory : false
- type : boolean
- name : mode_forward
- default : false
- mandatory : false
- type : boolean
- name : mode_reverse
- default : false
- mandatory : false
- type : boolean
- name : best
- default : false
- mandatory : false
- type : boolean
- name : space
- default : 10.0
- mandatory : false
- type : float
- name : seed
- default : 20825
- mandatory : false
- type : long
- name : align
- default : false
- mandatory : false
- type : boolean
- name : width
- default : 50
- mandatory : false
- type : long
- analysis :
License(s): No info yet Login to add license info Cost: No info yet Login to add cost info Usage conditions: No info yet Login to add usage conditions info Contact info: No info yet Login to add contact info How to cite this service: No info yet Login to add how to cite info Publications about this service: for this service (this can be in a common citation format like Bibtex, MLA or APA, a DOI, a URL, etc.) No info yet Login to add publications info Citations of this service: No info yet Login to add citations info Example workflows using this service: See all workflows on myExperiment that use this service Login to add workflows info