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EBIEMBL-EBI Web Servicesservicesmsaprank_soap
Table of Contents

PRANK (SOAP)

Description

PRANK 1) is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

For more information see:

Web service registry entries:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the EMBL-EBI's Terms of Use.

WSDL

The WSDL for the PRANK SOAP service: http://www.ebi.ac.uk/Tools/services/soap/prank?wsdl

Operations

getParameters()

Get a list of the parameter names.

Arguments: none

Returns: a list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameter.

Arguments:

  • parameterId: identifier/name of the parameter to fetch details of.

Returns: a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.

Arguments:

Returns: a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.

Arguments:

  • jobId: (required) job identifier.

Returns: a string containing the status.

The values for the status are:

  • RUNNING: the job is currently being processed.
  • FINISHED: job has finished, and the results can then be retrieved.
  • ERROR: an error occurred attempting to get the job status.
  • FAILURE: the job failed.
  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: JDispatcher.

getResultTypes(jobId)

Get the available result types for a finished job.

Arguments:

  • jobId: (required) job identifier.

Returns: a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.

Arguments:

  • jobId: (required) job identifier.
  • type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.
  • parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

Data Types

InputParameters

The input parameters for the job:

Attribute Type Description
sequence string sequences to align
data_file base64 sequences to align
tree_file base64 Tree file in Newick Binary Format.
do_njtree boolean Compute NJ guide tree from input alignment
do_clustalw_tree boolean Compute guide tree using ClustalW2
model_file base64 Structure Model File.
output_format string Format for output alignment file
trust_insertions boolean Trust inferred insertions and do not allow their later matching
show_insertions_with_dots boolean Show gaps created by insertions as dots, deletions as dashes
use_log_space boolean Use log space for probabilities; slower but necessary for large numbers of sequences
use_codon_model boolean Use codon substutition model for alignment; requires DNA, multiples of three in length
translate_DNA boolean Translate DNA sequences to proteins and backtranslate results
mt_translate_DNA boolean Translate DNA sequences to mt proteins, align and backtranslate results
gap_rate real Gap Opening Rate
gap_extension real Gap Extension Probability
tn93_kappa real Parameter kappa for Tamura-Nei DNA substitution model
tn93_rho real Parameter rho for Tamura-Nei DNA substitution model
guide_pairwise_distance real Fixed pairwise distance used for generating scoring matrix in guide tree computation
max_pairwise_distance real Maximum pairwise distance allowed in progressive steps of multiple alignment; allows making matching more stringent or flexible
branch_length_scaling real Factor for scaling all branch lengths
branch_length_fixed real Fixed value for all branch lengths
branch_length_maximum real Upper limit for branch lengths
use_real_branch_lengths boolean Use real branch lengths; using this can be harmful as scoring matrices became flat for large distances; rather use max_pairwise_distance
do_no_posterior boolean Do not compute posterior probability; much faster if those not needed
run_once boolean Do not iterate alignment
run_twice boolean Iterate alignment
penalise_terminal_gaps boolean Penalise terminal gaps as any other gap
do_posterior_only boolean Compute posterior probabilities for given aligned sequences; may be unstable but useful
use_chaos_anchors boolean Use chaos anchors to massively speed up alignments; DNA only
minimum_anchor_distance int Minimum chaos anchor distance
maximum_anchor_distance int Maximum chaos anchor distance
skip_anchor_distance int Chaos anchor skip distance
drop_anchor_distance int Chaos anchor drop distance
output_ancestors boolean Output ancestral sequences and probability profiles; note additional files
noise_level int Noise level; progress and debugging information
stay_quiet boolean Stay quiet; disable all progress information
random_seed int Set seed for random number generator; not recommended

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

wsParameterDetails

Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).

Attribute Type Description
name string Name of the parameter.
description string Description of the parameter, suitable for use in option help interfaces.
type string Data type of the parameter.
values list of wsParameterValue List of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

Attribute Type Description
label string Display name of the value, for use in interfaces.
value string String representation of the value to be passed to the tool parameter.
defaultValue boolean Flag indicating if this value is the default.
properties list of wsProperty List of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string
value string

wsRawOutputParameter

Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Attribute Type Description
name string
value list of string

wsResultType

Description of a result type. Returned by getResultTypes(jobId).

Attribute Type Description
identifier string Identifier for the result type. Passed as type to getResult(jobId, type, parameters).
label string Display name for use in user interfaces.
description string Description of the result type, for use in help interfaces.
mediaType string MIME type of the returned data.
fileSuffix string Suggested suffix for file name, if writing data to disk.
1) Löytynoja A. and Goldman N. (2005)
An algorithm for progressive multiple alignment of sequences with insertions.
Proc. Natl. Acad. Sci. USA 102:10557-10562
PubMed: 16000407
DOI: 10.1073/pnas.0409137102
 
services/msa/prank_soap.txt · Last modified: 2013/04/30 10:25 by hpm
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