ehmmbuild 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/hmm.ehmmbuild

WSDL Location:
http://www.ebi.ac.uk/soaplab/services/hmm.ehmmbuild?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 : ehmmbuild
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : HMM
      • description : Build a profile HMM from an alignment.
      • analysis_extension :
      • input :

Show all

  • ds_lsr_analysis :
    • analysis :
      • name : ehmmbuild
      • output :
      • installation : Soaplab2 default installation
      • version : 6.3.0
      • type : HMM
      • description : Build a profile HMM from an alignment.
      • 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 :
          • standard :
            • repeatable :
          • base :
          • standard :
            • list :
              • list_item :
                • shown_as : global-multidomain
                • level : 0
                • value : D
                • shown_as : local-multidomain
                • level : 0
                • value : F
                • shown_as : global-singledomain
                • level : 0
                • value : G
                • shown_as : local-singledomain
                • level : 0
                • value : S
              • name : Alignment preference
              • type : full
            • repeatable :
          • base :
          • 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 : %f
            • repeatable :
          • base :
            • name : pamwgt
            • ordering : 6
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Controls the weight on a PAM-based prior. Only has effect if -pam option is also in use. is a positive real number, 20.0 by default. is the number of ‘pseudocounts’ contriubuted by the heuristic prior. Very high values of can force a scoring system that is entirely driven by the substitution matrix, making HMMER somewhat approximate Gribskov profiles.
            • default : 20.0
            • qualifier : pamwgt
            • mandatory : false
            • prompt : Weighting for PAM.
            • type : float
          • range :
            • format : %d
            • repeatable :
          • base :
            • name : pbswitch
            • ordering : 12
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic integer
            • help : For alignments with a very large number of sequences, the GSC, BLOSUM, and Voronoi weighting schemes are slow; they’re O(N^2) for N sequences. Henikoff position-based weights (PB weights) are more effcient. At or above a certain threshold sequence number hmmbuild will switch from GSC, BLOSUM, or Voronoi weights to PB weights. To disable this switching behavior (at the cost of compute time, set to be something larger than the number of sequences in your alignment. is a positive integer; the default is 1000.
            • default : 1000
            • qualifier : pbswitch
            • mandatory : false
            • prompt : Threshold to switch to position-based weights.
            • type : long
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : archpri
            • ordering : 13
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : The value of the ‘architecture prior’ used by MAP architecture construction. This value is a probability between 0 and 1. This parameter governs a geometric prior distribution over model lengths. As ‘archpri’ increases, longer models are favored a priori. As ‘archpri’ decreases, it takes more residue conservation in a column to make a column a ‘consensus’ match column in the model architecture. The 0.85 default has been chosen empirically as a reasonable setting.
            • default : 0.85
            • qualifier : archpri
            • mandatory : false
            • prompt : Architecture prior
            • type : float
          • base :
            • name : binary
            • ordering : 14
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Write the HMM to file in HMMER binary format instead of readable ASCII text.
            • default : false
            • qualifier : binary
            • mandatory : false
            • prompt : Write HMM as binary.
            • type : boolean
          • base :
            • name : fast
            • ordering : 15
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Quickly and heuristically determine the architecture of the model by assigning all columns with more than a certain fraction of gap characters to insert states. By default this fraction is 0.5, and it can be changed using the –gapmax option. The default construction algorithm is a maximum a posteriori (MAP) algorithm, which is slower.
            • default : false
            • qualifier : fast
            • mandatory : false
            • prompt : Work in fast mode
            • type : boolean
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : gapmax
            • ordering : 16
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Controls the -fast model construction algorithm, but if -fast is not being used, has no effect. If a column has more than a fraction of gap symbols in it, it gets assigned to an insert column. is a frequency from 0 to 1, and by default is set to 0.5. Higher values of mean more columns get assigned to consensus, and models get longer; smaller values of mean fewer columns get assigned to consensus, and models get smaller.
            • default : 0.5
            • qualifier : gapmax
            • mandatory : false
            • prompt : Fast mode control
            • type : float
          • base :
            • name : hand
            • ordering : 17
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Specify the architecture of the model by hand: the alignment file must be in SELEX or Stockholm format, and the reference annotation line (RF in SELEX, GC RF in Stockholm) is used to specify the architecture. Any column marked with a non-gap symbol (such as an ‘x’, for instance) is assigned as a consensus (match) column in the model.
            • default : false
            • qualifier : hand
            • mandatory : false
            • prompt : Specify model by hand.
            • type : boolean
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : sidlevel
            • ordering : 18
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Controls both the determination of effective sequence number and the behavior of the -wblosum weighting option. The sequence alignment is clustered by percent identity, and the number of clusters at a cutoff threshold of is used to determine the effective sequence number. Higher values of give more clusters and higher effective sequence numbers; lower values of give fewer clusters and lower effective sequence numbers. is a fraction from 0 to 1, and by default is set to 0.62 (corresponding to the clustering level used in constructing the BLOSUM62 substitution matrix).
            • default : 0.62
            • qualifier : sidlevel
            • mandatory : false
            • prompt : Cutoff ID threhold
            • type : float
          • base :
            • name : noeff
            • ordering : 19
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Turn off the effective sequence number calculation, and use the true number of sequences instead. This will usually reduce the sensitivity of the final model (so don’t do it without good reason!)
            • default : false
            • qualifier : noeff
            • mandatory : false
            • prompt : Turn off the effective sequence number calculation.
            • type : boolean
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : swentry
            • ordering : 20
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Controls the total probability that is distributed to local entries into the model, versus starting at the beginning of the model as in a global alignment. is a probability from 0 to 1, and by default is set to 0.5. Higher values of mean that hits that are fragments on their left (N or 5′-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of mean that fragments on the left will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5’/3′) termini of your target sequences using –swentry and –swexit.
            • default : 0.5
            • qualifier : swentry
            • mandatory : false
            • prompt : Probability control for local entries
            • type : float
          • range :
            • format : %f
            • repeatable :
          • base :
            • name : swexit
            • ordering : 21
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic float
            • help : Controls the total probability that is distributed to local exits from the model, versus ending an alignment at the end of the model as in a global alignment. is a probability from 0 to 1, and by default is set to 0.5. Higher values of mean that hits that are fragments on their right (C or 3′-terminal) side will be penalized less, but complete global alignments will be penalized more. Lower values of mean that fragments on the right will be penalized more, and global alignments on this side will be favored. This option only affects the confgurations that allow local alignments, e.g. -s and -f; unless one of these options is also activated, this option has no effect. You have independent control over local/global alignment behavior for the N/C (5’/3′) termini of your target sequences using -swentry and -swexit.
            • default : 0.5
            • qualifier : swexit
            • mandatory : false
            • prompt : Probability control for exits
            • type : float
          • base :
            • name : verbosity
            • ordering : 22
            • option :
              • name : EDAM:
              • type : normal
              • value : Generic boolean
            • help : Print more possibly useful stuff, such as the individual scores for each sequence in the alignment.
            • default : false
            • qualifier : verbosity
            • mandatory : false
            • prompt : Verbosity.
            • type : boolean
          • standard :
            • list :
              • list_item :
                • shown_as : Blosum
                • level : 0
                • value : B
                • shown_as : Gerstein/Sonnhammer/Chothia
                • level : 0
                • value : G
                • shown_as : Krogh/Mitchison
                • level : 0
                • value : K
                • shown_as : Henikoff
                • level : 0
                • value : W
                • shown_as : Sibbald/Argos Voronoi
                • level : 0
                • value : V
                • shown_as : None
                • level : 0
                • value : N
              • name : Weighting method
              • type : full
            • repeatable :
          • base :
          • data :
            • result :
            • iotype : output
          • base :
          • data :
            • result :
            • iotype : output
          • base :
        • 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 : hmm
          • help_url : http://emboss.sourceforge.net/apps/release/6.3/emboss/apps/ehmmbuild.html
        • event :
          • action :
          • id : _E_1
      • input :
        • name : pamwgt
        • default : 20.0
        • mandatory : false
        • type : float
        • name : pbswitch
        • default : 1000
        • mandatory : false
        • type : long
        • name : archpri
        • default : 0.85
        • mandatory : false
        • type : float
        • name : binary
        • default : false
        • mandatory : false
        • type : boolean
        • name : fast
        • default : false
        • mandatory : false
        • type : boolean
        • name : gapmax
        • default : 0.5
        • mandatory : false
        • type : float
        • name : hand
        • default : false
        • mandatory : false
        • type : boolean
        • name : sidlevel
        • default : 0.62
        • mandatory : false
        • type : float
        • name : noeff
        • default : false
        • mandatory : false
        • type : boolean
        • name : swentry
        • default : 0.5
        • mandatory : false
        • type : float
        • name : swexit
        • default : 0.5
        • mandatory : false
        • type : float
        • name : verbosity
        • default : false
        • mandatory : false
        • type : boolean

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