This looks like a Soaplab service. Click here for more info and guidance on how to use this service )
About Soaplab
Soaplab services are command line applications, wrapped as SOAP services, and served from a Soaplab server. All Soaplab services have the same generic set of SOAP operations (depending on the Soaplab version) as they all share a standardised interface.
Certain tools, like the Taverna workflow workbench, provide automatic support for the Soaplab way of executing these services. In some cases you will need to use the Soaplab Server Base URL rather than the WSDL location in these tools.
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
- Sourceforge site for EMBOSS Soaplab services
Provider:
European Bioinformatics Institute (EMBL-EBI)
Location:
United Kingdom
Submitter/Source:
SoapLab Support (over 11 years ago)
Base URL:
http://www.ebi.ac.uk:80/soaplab/typed/services/nucleic_composition.compseq
WSDL Location:
http://www.ebi.ac.uk/soaplab/typed/services/nucleic_composition.compseq?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/compseq.html Login to add a documentation URL Description(s): from provider’s description doc (over 10 years ago) Calculate the composition of unique words in sequences
SoapLab Support(over 10 years ago)
Calculate the composition of unique words in sequences
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 : compseq
- installation : Soaplab2 default installation
- type : Nucleic Composition, Protein Composition
- output :
- description : Calculate the composition of unique words in sequences
- version : 6.1.0
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : compseq
- installation : Soaplab2 default installation
- type : Nucleic Composition, Protein Composition
- output :
- description : Calculate the composition of unique words in sequences
- 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 : nucleic_composition
- help_url : http://emboss.sourceforge.net/apps/release/6.1/emboss/apps/compseq.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 :
- range :
- format : %d
- max :
- min : 1
- repeatable :
- base :
- name : word
- help : This is the size of word (n-mer) to count. Thus if you want to count codon frequencies for a nucleotide sequence, you should enter 3 here.
- default : 2
- option :
- name : calculated_hardmax
- type : normal
- value : ${acdprotein}? 4 : 6
- name : scalemin
- type : style
- value : 1
- mandatory : false
- qualifier : word
- prompt : Word size to consider (e.g. 2=dimer)
- type : long
- ordering : 6
- data :
- result :
- extension : composition
- iotype : output
- base :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- max :
- min : 0
- repeatable :
- base :
- name : frame
- help : The normal behaviour of ‘compseq’ is to count the frequencies of all words that occur by moving a window of length ‘word’ up by one each time. This option allows you to move the window up by the length of the word each time, skipping over the intervening words. You can count only those words that occur in a single frame of the word by setting this value to a number other than zero. If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on.
- default : 0
- option :
- name : calculated_hardmax
- type : normal
- value : ${word}
- mandatory : false
- qualifier : frame
- prompt : Frame of word to look at (0=all frames)
- type : long
- ordering : 8
- base :
- name : ignorebz
- help : The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of ‘Other’ words.
- default : false
- mandatory : false
- qualifier : ignorebz
- prompt : Ignore the amino acids B and Z and just count them as ‘Other’
- type : boolean
- ordering : 9
- base :
- name : reverse
- help : Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence.
- default : false
- mandatory : false
- qualifier : reverse
- prompt : Count words in the forward and reverse sense
- type : boolean
- ordering : 10
- base :
- name : calcfreq
- help : If this is set true then the expected frequencies of words are calculated from the observed frequency of single bases or residues in the sequences. If you are reporting a word size of 1 (single bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency. Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if ‘calcfreq’ is set to be true.
- default : false
- mandatory : false
- qualifier : calcfreq
- prompt : Calculate expected frequency from sequence
- type : boolean
- ordering : 11
- base :
- name : zerocount
- help : You can make the output results file much smaller if you do not display the words with a zero count.
- default : false
- mandatory : false
- qualifier : zerocount
- prompt : Display the words that have a frequency of zero
- type : boolean
- ordering : 15
- data :
- option :
- input :
- name : word
- default : 2
- mandatory : false
- type : long
- name : frame
- default : 0
- mandatory : false
- type : long
- name : ignorebz
- default : false
- mandatory : false
- type : boolean
- name : reverse
- default : false
- mandatory : false
- type : boolean
- name : calcfreq
- default : false
- mandatory : false
- type : boolean
- name : zerocount
- default : false
- mandatory : false
- type : boolean
- analysis :
License(s): No info yet Login to add license info Cost: No info yet Login to add cost info Usage conditions: No info yet Login to add usage conditions info Contact info: No info yet Login to add contact info How to cite this service: No info yet Login to add how to cite info Publications about this service: for this service (this can be in a common citation format like Bibtex, MLA or APA, a DOI, a URL, etc.) No info yet Login to add publications info Citations of this service: No info yet Login to add citations info Example workflows using this service: See all workflows on myExperiment that use this service Login to add workflows info