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Further documentation on Soaplab services is available:
- Soaplab overview
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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/alignment_consensus.cons
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/alignment_consensus.cons?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 : cons
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Consensus
- description : Create a consensus sequence from a multiple alignment
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : cons
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Consensus
- description : Create a consensus sequence from a multiple alignment
- 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 :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- repeatable :
- base :
- name : plurality
- ordering : 6
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- name : calculated_default
- type : normal
- value : ${sequence.totweight} / 2
- help : Set a cut-off for the number of positive matches below which there is no consensus. The default plurality is taken as half the total weight of all the sequences in the alignment.
- qualifier : plurality
- mandatory : false
- prompt : Plurality check value
- type : float
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : identity
- ordering : 7
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- help : Provides the facility of setting the required number of identities at a site for it to give a consensus at that position. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus.
- default : 0
- qualifier : identity
- mandatory : false
- prompt : Required number of identities at a position
- type : long
- range :
- format : %f
- repeatable :
- base :
- name : setcase
- ordering : 8
- option :
- name : EDAM:0002146
- type : normal
- value : data Threshold
- name : calculated_default
- type : normal
- value : ${sequence.totweight} / 2
- help : Sets the threshold for the positive matches above which the consensus is is upper-case and below which the consensus is in lower-case.
- qualifier : setcase
- mandatory : false
- prompt : Define a threshold above which the consensus is given in uppercase
- type : float
- data :
- result :
- iotype : output
- base :
- standard :
- repeatable :
- 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:0000187
- type : normal
- value : topic Sequence alignment analysis
- name : EDAM:0000448
- type : normal
- value : operation Sequence alignment conservation analysis
- 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 : alignment_consensus
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/cons.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : identity
- default : 0
- mandatory : false
- type : long
- analysis :
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