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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:
Mike Mayer (over 9 years ago)
Base URL:
http://www.ebi.ac.uk/soaplab/services/hmm.ehmmpfam
WSDL Location:
http://www.ebi.ac.uk/soaplab/services/hmm.ehmmpfam?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 : ehmmpfam
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : HMM
- description : Search one or more sequences against an HMM database.
- analysis_extension :
- input :
- analysis :
- ds_lsr_analysis :
- analysis :
- name : ehmmpfam
- output :
- installation : Soaplab2 default installation
- version : 6.3.0
- type : HMM
- description : Search one or more sequences against an HMM database.
- 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 :
- data :
- ioformat : unspecified
- iotype : input
- repeatable :
- base :
- range :
- format : %d
- repeatable :
- base :
- name : a
- ordering : 5
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- help : Limits the alignment output to the best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files.
- default : 100
- qualifier : a
- mandatory : false
- prompt : Limit output to best-scoring domains.
- type : long
- range :
- format : %f
- repeatable :
- base :
- name : e
- ordering : 6
- option :
- name : EDAM:
- type : normal
- value : Generic float
- help : Set the E-value cutoff for the per-sequence ranked hit list to , where is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown.
- default : 10.
- qualifier : e
- mandatory : false
- prompt : E-value cutoff
- type : float
- data :
- result :
- iotype : output
- base :
- base :
- name : nuc
- ordering : 8
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can’t reliably determine the correct ‘alphabet’ by itself.
- default : false
- qualifier : nuc
- mandatory : false
- prompt : Set models and sequence to nucleic
- type : boolean
- range :
- format : %f
- repeatable :
- base :
- name : t
- ordering : 9
- option :
- name : EDAM:
- type : normal
- value : Generic float
- help : Set the bit score cutoff for the per-sequence ranked hit list to , where is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown.
- default : -1000000.
- qualifier : t
- mandatory : false
- prompt : Bit score cutoff
- type : float
- range :
- format : %d
- repeatable :
- base :
- name : z
- ordering : 10
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- help : Calculate the E-value scores as if we had seen a sequence database of sequences. The default is arbitrarily set to 59021, the size of Swissprot 34.
- default : 59021
- qualifier : z
- mandatory : false
- prompt : Calculate E-value for fixed database size
- type : long
- base :
- name : acc
- ordering : 13
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database.
- default : false
- qualifier : acc
- mandatory : false
- prompt : Report accessions.
- type : boolean
- base :
- name : compat
- ordering : 14
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don’t have to be rewritten.
- default : false
- qualifier : compat
- mandatory : false
- prompt : Use HMMER 2.1.1 output format.
- type : boolean
- range :
- format : %d
- repeatable :
- base :
- name : cpu
- ordering : 15
- option :
- name : EDAM:
- type : normal
- value : Generic integer
- help : Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).
- default : 0
- qualifier : cpu
- mandatory : false
- prompt : Number of CPUs
- type : long
- base :
- name : cutga
- ordering : 16
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT -domT , but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn’t work.
- default : false
- qualifier : cutga
- mandatory : false
- prompt : Use Pfam GA (gathering threshold) score cutoffs.
- type : boolean
- base :
- name : cuttc
- ordering : 17
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT -domT , but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn’t work.
- default : false
- qualifier : cuttc
- mandatory : false
- prompt : Use Pfam TC (trusted cutoff) score cutoffs.
- type : boolean
- base :
- name : cutnc
- ordering : 18
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT -domT , but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn’t work.
- default : false
- qualifier : cutnc
- mandatory : false
- prompt : Use Pfam NC (noise cutoff) score cutoffs.
- type : boolean
- range :
- format : %f
- repeatable :
- base :
- name : dome
- ordering : 19
- option :
- name : EDAM:
- type : normal
- value : Generic float
- help : Set the E-value cutoff for the per-domain ranked hit list to , where is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list.
- default : 1000000.
- qualifier : dome
- mandatory : false
- prompt : E-value domain cutoff
- type : float
- range :
- format : %f
- repeatable :
- base :
- name : domt
- ordering : 20
- option :
- name : EDAM:
- type : normal
- value : Generic float
- help : Set the bit score cutoff for the per-domain ranked hit list to , where is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by –domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users’ Guide for more detail.
- default : -1000000.
- qualifier : domt
- mandatory : false
- prompt : Bit score domain cutoff
- type : float
- base :
- name : forward
- ordering : 21
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however.
- default : false
- qualifier : forward
- mandatory : false
- prompt : Use forward algorithm
- type : boolean
- base :
- name : nulltwo
- ordering : 22
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases –null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through.
- default : false
- qualifier : nulltwo
- mandatory : false
- prompt : Turn off second null model
- type : boolean
- base :
- name : pvm
- ordering : 23
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function.
- default : false
- qualifier : pvm
- mandatory : false
- prompt : Use parallel virtual machine
- type : boolean
- base :
- name : xnu
- ordering : 24
- option :
- name : EDAM:
- type : normal
- value : Generic boolean
- help : Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model.
- default : false
- qualifier : xnu
- mandatory : false
- prompt : Use XNU filtering
- type : boolean
- data :
- 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/ehmmpfam.html
- event :
- action :
- id : _E_1
- parameter :
- input :
- name : a
- default : 100
- mandatory : false
- type : long
- name : e
- default : 10.
- mandatory : false
- type : float
- name : nuc
- default : false
- mandatory : false
- type : boolean
- name : t
- default : -1000000.
- mandatory : false
- type : float
- name : z
- default : 59021
- mandatory : false
- type : long
- name : acc
- default : false
- mandatory : false
- type : boolean
- name : compat
- default : false
- mandatory : false
- type : boolean
- name : cpu
- default : 0
- mandatory : false
- type : long
- name : cutga
- default : false
- mandatory : false
- type : boolean
- name : cuttc
- default : false
- mandatory : false
- type : boolean
- name : cutnc
- default : false
- mandatory : false
- type : boolean
- name : dome
- default : 1000000.
- mandatory : false
- type : float
- name : domt
- default : -1000000.
- mandatory : false
- type : float
- name : forward
- default : false
- mandatory : false
- type : boolean
- name : nulltwo
- default : false
- mandatory : false
- type : boolean
- name : pvm
- default : false
- mandatory : false
- type : boolean
- name : xnu
- default : false
- mandatory : false
- type : boolean
- analysis :
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