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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.esim4
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/alignment_global.esim4?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/esim4.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Align an mRNA to a genomic DNA sequence
SoapLab Support(over 10 years ago)
Align an mRNA to a 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 : esim4
- installation : Soaplab2 default installation
- type : Alignment Global
- output :
- description : Align an mRNA to a genomic DNA sequence
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : esim4
- installation : Soaplab2 default installation
- type : Alignment Global
- output :
- description : Align an mRNA to a 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/esim4.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 : word
- default : 12
- mandatory : false
- qualifier : word
- prompt : Sets the word size (W) for blast hits. Default value: 12.
- type : long
- ordering : 5
- range :
- format : %d
- repeatable :
- base :
- name : extend
- default : 12
- mandatory : false
- qualifier : extend
- prompt : Sets the word extension termination limit (X) for the blast-like stage of the algorithm. Default value: 12.
- type : long
- ordering : 6
- range :
- format : %d
- max : 10
- repeatable :
- base :
- name : cutoff
- default : 3
- option :
- name : scalemax
- type : style
- value : 10
- mandatory : false
- qualifier : cutoff
- prompt : Sets the cutoff (E) in range [3,10].
- type : long
- ordering : 7
- base :
- name : useramsp
- default : false
- mandatory : false
- qualifier : useramsp
- prompt : False: esim4 calculates mspA, True: value from mspA command line argument.
- type : boolean
- ordering : 8
- range :
- format : %d
- repeatable :
- base :
- name : amsp
- help : MSP score threshold (K) for the first stage of the algorithm. (If this option is not specified, the threshold is computed from the lengths of the sequences, using statistical criteria.) For example, a good value for genomic sequences in the range of a few hundred Kb is 16. To avoid spurious matches, however, a larger value may be needed for longer sequences.
- default : 16
- mandatory : false
- qualifier : amsp
- prompt : MSP score threshold (K) for the first stage of the algorithm.
- type : long
- ordering : 9
- base :
- name : userbmsp
- default : false
- mandatory : false
- qualifier : userbmsp
- prompt : False: esim4 calculates mspB, True: value from mspB command line argument.
- type : boolean
- ordering : 10
- range :
- format : %d
- repeatable :
- base :
- name : bmsp
- help : Sets the threshold for the MSP scores (C) when aligning the as-yet-unmatched fragments, during the second stage of the algorithm. By default, the smaller of the constant 12 and a statistics-based threshold is chosen.
- default : 12
- mandatory : false
- qualifier : bmsp
- prompt : MSP score threshold (C) during the second stage of the algorithm.
- type : long
- ordering : 11
- range :
- format : %d
- repeatable :
- base :
- name : weight
- default : 0
- mandatory : false
- qualifier : weight
- prompt : Weight value (H) (undocumented). 0 uses a default, >0 is a value
- type : long
- ordering : 12
- range :
- format : %d
- repeatable :
- base :
- name : diagonal
- default : 10
- mandatory : false
- qualifier : diagonal
- prompt : Bound (K) for the diagonal distance within consecutive MSPs in an exon.
- type : long
- ordering : 13
- choice_list :
- separator : ,
- grouptype : zero_or_more
- base :
- name : strand_both
- default : true
- mandatory : false
- qualifier : both
- type : boolean
- prompt : Both strands
- ordering : 15
- name : strand_forward
- default : false
- mandatory : false
- qualifier : forward
- type : boolean
- prompt : Forward strand only
- ordering : 16
- name : strand_reverse
- default : false
- mandatory : false
- qualifier : reverse
- type : boolean
- prompt : Reverse strand only
- ordering : 17
- base :
- range :
- format : %d
- max : 5
- min : 0
- repeatable :
- base :
- name : format
- help : Sets the output format (A). Exon endpoints only (format=0), exon endpoints and boundaries of the coding region (CDS) in the genomic sequence, when specified for the input mRNA (-format=5), alignment text (-format=1), alignment in lav-block format (-format=2), or both exon endpoints and alignment text (-format=3 or -format=4). If a reverse complement match is found, -format=0,1,2,3,5 will give its position in the plus strand of the longer sequence and the minus strand of the shorter sequence. -format=4 will give its position in the plus strand of the first sequence (mRNA) and the minus strand of the second sequence (genome), regardless of which sequence is longer. The -format=5 option can be used with the S command line option to specify the endpoints of the CDS in the mRNA, and produces output in the exons file format required by PipMaker.
- default : 0
- option :
- name : scalemax
- type : style
- value : 5
- mandatory : false
- qualifier : format
- prompt : Output format (A)
- type : long
- ordering : 18
- base :
- name : cliptails
- help : Trim poly-A tails (P). Specifies whether or not the program should report the fragment of the alignment containing the poly-A tail (if found). By default (-nocliptails) the alignment is displayed as computed. When this feature is enabled (-cliptails), sim4 will remove the poly-A tails and all format options will produce additional lav alignment headers.
- default : false
- mandatory : false
- qualifier : cliptails
- prompt : Trim poly-A tails (P)
- type : boolean
- ordering : 19
- base :
- name : smallexons
- help : Requests an additional search for small marginal exons (N) (N=1) guided by the splice-site recognition signals. This option can be used when a high accuracy match is expected. The default value is N=0, specifying no additional search.
- default : false
- mandatory : false
- qualifier : smallexons
- prompt : Search for small marginal exons (N)
- type : boolean
- ordering : 20
- base :
- name : ambiguity
- help : Controls the set of characters allowed in the input sequences (B). By default (-ambiguity), ambiguity characters (ABCDGHKMNRSTVWXY) are allowed. By specifying -noambiguity, the set of acceptable characters is restricted to A,C,G,T,N and X only.
- default : false
- mandatory : false
- qualifier : ambiguity
- prompt : Disallow ambiguity characters (B)
- type : boolean
- ordering : 21
- standard :
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : aoffset
- mandatory : false
- qualifier : aoffset
- prompt : Undocumented (f) – some sort of offset in first sequence.
- type : long
- ordering : 23
- range :
- format : %d
- repeatable :
- base :
- name : boffset
- mandatory : false
- qualifier : boffset
- prompt : Undocumented (F) – some sort of offset in second sequence.
- type : long
- ordering : 24
- range :
- format : %d
- repeatable :
- base :
- name : toa
- mandatory : false
- qualifier : toa
- prompt : Undocumented (t)- offset end of first sequence?
- type : long
- ordering : 25
- range :
- format : %d
- repeatable :
- base :
- name : tob
- mandatory : false
- qualifier : tob
- prompt : Undocumented (T) – offset end of second sequence?
- type : long
- ordering : 26
- data :
- option :
- input :
- name : word
- default : 12
- mandatory : false
- type : long
- name : extend
- default : 12
- mandatory : false
- type : long
- name : cutoff
- default : 3
- mandatory : false
- type : long
- name : useramsp
- default : false
- mandatory : false
- type : boolean
- name : amsp
- default : 16
- mandatory : false
- type : long
- name : userbmsp
- default : false
- mandatory : false
- type : boolean
- name : bmsp
- default : 12
- mandatory : false
- type : long
- name : weight
- default : 0
- mandatory : false
- type : long
- name : diagonal
- default : 10
- mandatory : false
- type : long
- name : strand_both
- default : true
- mandatory : false
- type : boolean
- name : strand_forward
- default : false
- mandatory : false
- type : boolean
- name : strand_reverse
- default : false
- mandatory : false
- type : boolean
- name : format
- default : 0
- mandatory : false
- type : long
- name : cliptails
- default : false
- mandatory : false
- type : boolean
- name : smallexons
- default : false
- mandatory : false
- type : boolean
- name : ambiguity
- default : false
- mandatory : false
- type : boolean
- analysis :
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