ememe SOAP Soaplab

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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/protein_motifs.ememe

WSDL Location:
http://www.ebi.ac.uk/soaplab/services/protein_motifs.ememe?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 : ememe
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : Protein Motifs
      • description : Multiple EM for Motif Elicitation
      • analysis_extension :
      • input :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : ememe
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : Protein Motifs
      • description : Multiple EM for Motif Elicitation
      • 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
          • base :
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • data :
            • ioformat : unspecified
            • iotype : input
            • repeatable :
          • base :
          • standard :
            • list :
              • list_item :
                • level : 0
                • value : oops
                • level : 0
                • value : zoops
                • level : 0
                • value : anr
              • name : Distribution of motifs
              • type : full
            • repeatable :
          • base :
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : nmotifs
            • ordering : 9
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The number of *different* motifs to search for. MEME will search for and output motifs.
            • default : 1
            • qualifier : nmotifs
            • mandatory : false
            • prompt : Maximum number of motifs to find
            • type : long
          • base :
            • name : text
            • ordering : 10
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Default output is in HTML
            • default : false
            • qualifier : text
            • mandatory : false
            • prompt : Output in text format (default is HTML)
            • type : boolean
          • standard :
            • list :
              • list_item :
                • level : 0
                • value : dirichlet
                • level : 0
                • value : dmix
                • level : 0
                • value : mega
                • level : 0
                • value : megap
                • level : 0
                • value : addone
              • name : Prior
              • type : full
            • repeatable :
          • base :
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : evt
            • ordering : 12
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Quit looking for motifs if E-value exceeds this value. Has an extremely high default so by default MEME never quits before -nmotifs have been found. A value of -1 here is a shorthand for infinity.
            • default : -1
            • qualifier : evt
            • mandatory : false
            • prompt : Threshold value of motif E-value at which to stop searching.
            • type : float
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : nsites
            • ordering : 13
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for -nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between -minsites and -maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for -minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of -minsites is equal to sqrt(number sequences). The hardcoded default value of -maxsites is equal to the number of sequences (zoops) or MIN(5* num.sequences, 50) (anr). A value of -1 here represents nsites being unspecified.
            • default : -1
            • qualifier : nsites
            • mandatory : false
            • prompt : Number of sites for each motif
            • type : long
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : minsites
            • ordering : 14
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for -nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between -minsites and -maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for -minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of -minsites is equal to sqrt(number sequences). The hardcoded default value of -maxsites is equal to the number of sequences (zoops) or MIN(5 * num.sequences, 50) (anr). A value of -1 here represents minsites being unspecified.
            • default : -1
            • qualifier : minsites
            • mandatory : false
            • prompt : Minimum number of sites for each motif
            • type : long
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : maxsites
            • ordering : 15
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : These switches are ignored if mod = oops. The (expected) number of occurrences of each motif. If a value for -nsites is specified, only that number of occurrences is tried. Otherwise, numbers of occurrences between -minsites and -maxsites are tried as initial guesses for the number of motif occurrences. If a value is not specified for -minsites and maxsites then the default hardcoded into MEME, as opposed to the default value given in the ACD file, is used. The hardcoded default value of -minsites is equal to sqrt(number sequences). The hardcoded default value of -maxsites is equal to the number of sequences (zoops) or MIN(5 * num.sequences, 50) (anr). A value of -1 here represents maxsites being unspecified.
            • default : -1
            • qualifier : maxsites
            • mandatory : false
            • prompt : Maximum number of sites for each motif
            • type : long
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : wnsites
            • ordering : 16
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : The weight of the prior on nsites. This controls how strong the bias towards motifs with exactly nsites sites (or between minsites and maxsites sites) is. It is a number in the range [0..1). The larger it is, the stronger the bias towards motifs with exactly nsites occurrences is.
            • default : 0.8
            • qualifier : wnsites
            • mandatory : false
            • prompt : Weight on expected number of sites
            • type : float
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : w
            • ordering : 17
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The width of the motif(s) to search for. If -w is given, only that width is tried. Otherwise, widths between -minw and -maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value. A value of -1 here represents -w being unspecified.
            • default : -1
            • qualifier : w
            • mandatory : false
            • prompt : Motif width
            • type : long
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : minw
            • ordering : 18
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The width of the motif(s) to search for. If -w is given, only that width is tried. Otherwise, widths between -minw and -maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value.
            • default : 8
            • qualifier : minw
            • mandatory : false
            • prompt : Minumum motif width
            • type : long
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : maxw
            • ordering : 19
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The width of the motif(s) to search for. If -w is given, only that width is tried. Otherwise, widths between -minw and -maxw are tried. Note: if width is less than the length of the shortest sequence in the dataset, width is reset by MEME to that value.
            • default : 50
            • qualifier : maxw
            • mandatory : false
            • prompt : Maximum motif width
            • type : long
          • base :
            • name : nomatrim
            • ordering : 20
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : The -nomatrim, -wg, -ws and -noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying -nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches -wg (gap cost), -ws (space cost) and -noendgaps (do not penalize endgaps). See application documentation for further information.
            • default : false
            • qualifier : nomatrim
            • mandatory : false
            • prompt : Do not adjust motif width using multiple alignment.
            • type : boolean
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : wg
            • ordering : 21
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The -nomatrim, -wg, -ws and -noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying -nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches -wg (gap cost), -ws (space cost) and -noendgaps (do not penalize endgaps). See application documentation for further information.
            • default : 11
            • qualifier : wg
            • mandatory : false
            • prompt : Gap opening cost for multiple alignments
            • type : long
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : ws
            • ordering : 22
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The -nomatrim, -wg, -ws and -noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying -nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches -wg (gap cost), -ws (space cost) and -noendgaps (do not penalize endgaps). See application documentation for further information.
            • default : 1
            • qualifier : ws
            • mandatory : false
            • prompt : Gap extension cost for multiple alignments
            • type : long
          • base :
            • name : noendgaps
            • ordering : 23
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : The -nomatrim, -wg, -ws and -noendgaps switches control trimming (shortening) of motifs using the multiple alignment method. Specifying -nomatrim causes MEME to skip this and causes the other switches to be ignored. The pairwise alignment is controlled by the switches -wg (gap cost), -ws (space cost) and -noendgaps (do not penalise endgaps). See application documentation for further information.
            • default : false
            • qualifier : noendgaps
            • mandatory : false
            • prompt : Do not penalise end gaps in multiple alignments
            • type : boolean
          • base :
            • name : revcomp
            • ordering : 24
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Motif occurrences may be on the given DNA strand or on its reverse complement. The default is to look for DNA motifs only on the strand given in the training set.
            • default : false
            • qualifier : revcomp
            • mandatory : false
            • prompt : Allow sites on + or – DNA strands
            • type : boolean
          • base :
            • name : pal
            • ordering : 25
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Choosing -pal causes MEME to look for palindromes in DNA datasets. MEME averages the letter frequencies in corresponding columns of the motif (PSPM) together. For instance, if the width of the motif is 10, columns 1 and 10, 2 and 9, 3 and 8, etc., are averaged together. The averaging combines the frequency of A in one column with T in the other, and the frequency of C in one column with G in the other.
            • default : false
            • qualifier : pal
            • mandatory : false
            • prompt : Look for palindromes (requires input sequence to be dna)
            • type : boolean
          • base :
            • name : nostatus
            • ordering : 26
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Set this option to prevent progress reports to the terminal.
            • default : false
            • qualifier : nostatus
            • mandatory : false
            • prompt : Do not print progress reports to terminal
            • type : boolean
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : maxiter
            • ordering : 29
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : The number of iterations of EM to run from any starting point. EM is run for iterations or until convergence (see -distance, below) from each starting point.
            • default : 50
            • qualifier : maxiter
            • mandatory : false
            • prompt : Maximum EM iterations to run
            • type : long