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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
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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/protein_motifs.emast
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/protein_motifs.emast?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 : emast
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Motif detection
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : emast
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Protein Motifs
- description : Motif detection
- analysis_extension :
- parameter :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %f
- repeatable :
- base :
- name : ev
- ordering : 8
- option :
- name : EDAM:
- type : normal
- value : Generic float
- default : 10
- qualifier : ev
- mandatory : false
- prompt : Print results for sequences with E-value
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : mt
- ordering : 9
- option :
- name : EDAM:
- type : normal
- value : Generic float
- default : 0.0001
- qualifier : mt
- mandatory : false
- prompt : Show motif matches with p-value < mt
- type : float
- data :
- result :
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : smax
- ordering : 11
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- default : -1
- qualifier : smax
- mandatory : false
- prompt : Print results for no more than sequences
- type : long
- base :
- name : stdin
- ordering : 12
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : The default is to read the database specified inside .
- default : false
- qualifier : stdin
- mandatory : false
- prompt : Read database from standard input
- type : boolean
- base :
- name : text
- ordering : 13
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Default is hypertext (HTML) format
- default : false
- qualifier : text
- mandatory : false
- prompt : Output in text (ASCII) format
- type : boolean
- base :
- name : dna
- ordering : 14
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : dna
- mandatory : false
- prompt : Translate DNA sequences to protein
- type : boolean
- base :
- name : comp
- ordering : 15
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : The random model uses the letter frequencies in the current target sequence instead of the non-redundant database frequencies. This causes p-values and E-values to be compensated individually for the actual composition of each sequence in the database. This option can increase search time substantially due to the need to compute a different score distribution for each high-scoring sequence.
- default : false
- qualifier : comp
- mandatory : false
- prompt : Adjust p-values and E-values for sequence composition
- type : boolean
- range :
- format : %d
- repeatable :
- base :
- name : rank
- ordering : 16
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- default : -1
- qualifier : rank
- mandatory : false
- prompt : Print results starting with best
- type : long
- base :
- name : best
- ordering : 17
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : best
- mandatory : false
- prompt : Include only the best motif in diagrams
- type : boolean
- base :
- name : remcorr
- ordering : 18
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : remcorr
- mandatory : false
- prompt : Remove highly correlated motifs from query
- type : boolean
- base :
- name : brief
- ordering : 19
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : brief
- mandatory : false
- prompt : Brief output: do not print documentation.
- type : boolean
- base :
- name : b
- ordering : 20
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : b
- mandatory : false
- prompt : Print only sections I and II
- type : boolean
- base :
- name : nostatus
- ordering : 21
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : nostatus
- mandatory : false
- prompt : Do not print progress report
- type : boolean
- base :
- name : hitlist
- ordering : 22
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : If you specify the -hitlist switch to MAST, the motif ‘diagram’ takes the form of a comma separated list of motif occurrences (‘hits’). Each ‘hit’ has the format: where is the strand (+ or – for DNA, blank for protein), is the motif number, is the starting position of the hit, is the ending position of the hit, and is the position p-value of the hit.
- default : false
- qualifier : hitlist
- mandatory : false
- prompt : Print hit_list instead of diagram; implies -text
- type : boolean
- range :
- format : %d
- repeatable :
- base :
- name : c
- ordering : 25
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- default : -1
- qualifier : c
- mandatory : false
- prompt : Only use the first motifs
- type : long
- base :
- name : sep
- ordering : 26
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : sep
- mandatory : false
- prompt : Score reverse complement DNA strand as a separate sequence
- type : boolean
- base :
- name : norc
- ordering : 27
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : norc
- mandatory : false
- prompt : Do not score reverse complement DNA strand
- type : boolean
- base :
- name : w
- ordering : 28
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- default : false
- qualifier : w
- mandatory : false
- prompt : Show weak matches (mt type : boolean
- base :
- name : seqp
- ordering : 29
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : The default is to use POSITION p-values.
- default : false
- qualifier : seqp
- mandatory : false
- prompt : Use SEQUENCE p-values for motif thresholds
- type : boolean
- standard :
- repeatable :
- base :
- standard :
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : minseqs
- ordering : 32
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- default : -1
- qualifier : minseqs
- mandatory : false
- prompt : Lower bound on number of sequences in db
- type : long
- range :
- format : %f
- repeatable :
- base :
- name : mev
- ordering : 33
- option :
- name : EDAM:
- type : normal
- value : Generic float
- default : -1
- qualifier : mev
- mandatory : false
- prompt : Use only motifs with E-values less than
- type : float
- range :
- format : %d
- repeatable :
- base :
- name : m
- ordering : 34
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- help : Overrides value set by using -mev.
- default : -1
- qualifier : m
- mandatory : false
- prompt : Use only motif(s) number
- type : long
- standard :
- repeatable :
- base :
- data :
- option :
- 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 : protein_motifs
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/emast.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : ev
- default : 10
- mandatory : false
- type : float
- name : mt
- default : 0.0001
- mandatory : false
- type : float
- name : smax
- default : -1
- mandatory : false
- type : long
- name : stdin
- default : false
- mandatory : false
- type : boolean
- name : text
- default : false
- mandatory : false
- type : boolean
- name : dna
- default : false
- mandatory : false
- type : boolean
- name : comp
- default : false
- mandatory : false
- type : boolean
- name : rank
- default : -1
- mandatory : false
- type : long
- name : best
- default : false
- mandatory : false
- type : boolean
- name : remcorr
- default : false
- mandatory : false
- type : boolean
- name : brief
- default : false
- mandatory : false
- type : boolean
- name : b
- default : false
- mandatory : false
- type : boolean
- name : nostatus
- default : false
- mandatory : false
- type : boolean
- name : hitlist
- default : false
- mandatory : false
- type : boolean
- name : c
- default : -1
- mandatory : false
- type : long
- name : sep
- default : false
- mandatory : false
- type : boolean
- name : norc
- default : false
- mandatory : false
- type : boolean
- name : w
- default : false
- mandatory : false
- type : boolean
- name : seqp
- default : false
- mandatory : false
- type : boolean
- name : minseqs
- default : -1
- mandatory : false
- type : long
- name : mev
- default : -1
- mandatory : false
- type : float
- name : m
- default : -1
- mandatory : false
- type : long
- analysis :
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