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Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
UNITED KINGDOM
Submitter/Source:
Gilles (over 8 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/alignment_global.needleall
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/alignment_global.needleall?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 : needleall
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Global
- description : Many-to-many pairwise alignments of two sequence sets
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : needleall
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Alignment Global
- description : Many-to-many pairwise alignments of two sequence sets
- 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 :
- 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 :
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : gapopen
- ordering : 7
- option :
- name : EDAM:0001397
- type : normal
- value : data Gap opening penalty
- name : calculated_default
- type : normal
- value : ${acdprotein}? 10.0 : 10.0
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- help : The gap open 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 EDNAFULL matrix for nucleotide sequences.
- qualifier : gapopen
- mandatory : false
- prompt : Gap opening penalty
- type : float
- range :
- format : %f
- max : 10.0
- min : 0.0
- repeatable :
- base :
- name : gapextend
- ordering : 8
- option :
- name : EDAM:0001398
- type : normal
- value : data Gap extension penalty
- name : calculated_default
- type : normal
- value : ${acdprotein}? 0.5 : 0.5
- name : scalemax
- type : style
- value : 10.0
- name : scalemin
- type : style
- value : 0.0
- help : 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. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring.
- qualifier : gapextend
- mandatory : false
- prompt : Gap extension penalty
- type : float
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- base :
- name : endweight
- ordering : 10
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- default : false
- qualifier : endweight
- mandatory : false
- prompt : Apply end gap penalties.
- type : boolean
- range :
- format : %f
- max : 100.0
- min : 0.0
- repeatable :
- base :
- name : endopen
- ordering : 11
- option :
- name : EDAM:0001410
- type : normal
- value : data Terminal gap opening penalty
- name : calculated_default
- type : normal
- value : ${acdprotein}? 10.0 : 10.0
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : 0.0
- help : The end gap open penalty is the score taken away when an end 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 EDNAFULL matrix for nucleotide sequences.
- qualifier : endopen
- mandatory : false
- prompt : End gap opening penalty
- type : float
- range :
- format : %f
- max : 10.0
- min : 0.0
- repeatable :
- base :
- name : endextend
- ordering : 12
- option :
- name : EDAM:0001411
- type : normal
- value : data Terminal gap extension penalty
- name : calculated_default
- type : normal
- value : ${acdprotein}? 0.5 : 0.5
- name : scalemax
- type : style
- value : 10.0
- name : scalemin
- type : style
- value : 0.0
- help : The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap.
- qualifier : endextend
- mandatory : false
- prompt : End gap extension penalty
- type : float
- range :
- format : %f
- max : 100.0
- min : -10.0
- repeatable :
- base :
- name : minscore
- ordering : 13
- option :
- name : EDAM:0001772
- type : normal
- value : data Score
- name : scalemax
- type : style
- value : 100.0
- name : scalemin
- type : style
- value : -10.0
- help : Minimum alignment score to report an alignment.
- default : 0
- qualifier : minscore
- mandatory : false
- prompt : Minimum alignment score
- type : float
- base :
- name : brief
- ordering : 16
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : Brief identity and similarity
- default : false
- qualifier : brief
- mandatory : false
- prompt : Brief identity and similarity
- type : boolean
- data :
- result :
- iotype : output
- base :
- data :
- option :
- name : EDAM:0000185
- type : normal
- value : topic Pairwise sequence alignment
- name : EDAM:0000494
- type : normal
- value : operation Global pairwise sequence alignment
- 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_global
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/needleall.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : endweight
- default : false
- mandatory : false
- type : boolean
- name : minscore
- default : 0
- mandatory : false
- type : float
- name : brief
- default : false
- mandatory : false
- type : boolean
- analysis :
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