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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/edit.trimest
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/edit.trimest?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 : trimest
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove poly-A tails from nucleotide sequences
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : trimest
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : Edit
- description : Remove poly-A tails from nucleotide sequences
- 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 :
- range :
- format : %d
- min : 1
- repeatable :
- base :
- name : minlength
- ordering : 4
- option :
- name : EDAM:0001249
- type : normal
- value : data Sequence length
- name : scalemin
- type : style
- value : 1
- help : This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. If there are mismatches in the tail than there must be at least this length of poly-A tail before the mismatch for the mismatch to be considered part of the tail.
- default : 4
- qualifier : minlength
- mandatory : false
- prompt : Minimum length of a poly-A tail
- type : long
- range :
- format : %d
- min : 0
- repeatable :
- base :
- name : mismatches
- ordering : 5
- option :
- name : EDAM:0001773
- type : normal
- value : data Tool-specific parameter
- help : If there are this number or fewer contiguous non-A bases in a poly-A tail then, if there are ‘-minlength’ ‘A’ bases before them, they will be considered part of the tail and removed . For example the terminal 4 A’s of GCAGAAAA would be removed with the default values of -minlength=4 and -mismatches=1 (There are not at least 4 A’s before the last ‘G’ and so only the A’s after it are considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least -minlength A’s preceeding the last ‘G’, so it is part of the tail.
- default : 1
- qualifier : mismatches
- mandatory : false
- prompt : Number of contiguous mismatches allowed in a tail
- type : long
- base :
- name : reverse
- ordering : 6
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : When a poly-T region at the 5′ end of the sequence is found and removed, it is likely that the sequence is in the reverse sense. This option will change the sequence to the forward sense when it is written out. If this option is not set, then the sense will not be changed.
- default : false
- qualifier : reverse
- mandatory : false
- prompt : Write the reverse complement when poly-T is removed
- type : boolean
- base :
- name : tolower
- ordering : 7
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : The poly-A region can be ‘masked’ by converting the sequence characters to lower-case. Some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the ‘-supper’ sequence qualifier.
- default : false
- qualifier : tolower
- mandatory : false
- prompt : Change poly-A tail to lower-case
- type : boolean
- base :
- name : fiveprime
- ordering : 10
- option :
- name : EDAM:0002135
- type : normal
- value : data Toggle
- help : If this is set true, then the 5′ end of the sequence is inspected for poly-T tails. These will be removed if they are longer than any 3′ poly-A tails. If this is false, then the 5′ end is ignored.
- default : false
- qualifier : fiveprime
- mandatory : false
- prompt : Remove poly-T tails at the 5′ end of the sequence.
- type : boolean
- data :
- result :
- iotype : output
- 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:0000105
- type : normal
- value : topic Nucleic acid sequence features
- name : EDAM:0000363
- type : normal
- value : operation Sequence reverse and complement
- name : EDAM:0000369
- type : normal
- value : operation Sequence cutting
- name : EDAM:0000428
- type : normal
- value : operation PolyA signal identification
- 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 : edit
- help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/trimest.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : minlength
- default : 4
- mandatory : false
- type : long
- name : mismatches
- default : 1
- mandatory : false
- type : long
- name : reverse
- default : false
- mandatory : false
- type : boolean
- name : tolower
- default : false
- mandatory : false
- type : boolean
- name : fiveprime
- default : false
- mandatory : false
- type : boolean
- analysis :
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