Pratt (SOAP)


Pratt 1) 2) searches for patterns conserved in sets of unaligned protein sequences.

For more information see:


We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 30 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.


Sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

Language Download Requirements
C# .NET Executable: PrattCliClient.exe; Source: AbstractWsClient.cs, PrattClient.cs, PrattCliClient.cs A .NET runtime environment. If building from source development tools are also required. See the .NET tutorial for details.
Java Executable jar: Pratt_Axis1.jar; Source:, Axis 1.4; All dependencies, including Axis 1.4 and Commons-CLI, are available in
Perl SOAP::Lite

For further details of these tool-kits and workflow platforms see our Guide to Web Services.


The WSDL for the Pratt (SOAP) service:



Get a list of the parameter names.

Arguments: none

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


Get details of a specific parameter.


  • 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.


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


Get the status of a submitted job.


  • 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.


Get the available result types for a finished job.


  • 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.


  • 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


The input parameters for the job:

Attribute Type Description
minPerc int Minimum percentage of input sequences to match.
patternPosition string Pattern position in sequence.
maxPatternLength int Max pattern length.
maxNumPatternSymbols int Maximum number Of pattern symbols.
maxNumWildcard int Maximum length of a widecard (x).
maxNumFlexSpaces int Maximum length of flexible spaces.
maxFlexibility int Maximum flexibility.
maxFlexProduct int Maximum flex. product.
patternSymbolFile boolean Pattern symbol file.
numPatternSymbols int Number of pattern symbols used in the initial search.
patternScoring string Pattern scoring.
patternGraph string Pattern graph allows the use of an alignment or a query sequence to restrict the pattern search.
searchGreediness int the greediness of the search.
patternRefinement boolean Pattern refinement.
genAmbigSymbols boolean Generalise ambiguous symbols.
patternFormat boolean PROSITE pattern format.
maxNumPatterns int Maximum number of patterns.
maxNumAlignments int Maximum number of alignments between 1 and 100.
printPatterns boolean Print Patterns in sequences .
printingRatio int Printing ratio.
printVertically boolean Print vertically.
stype string Input sequence type.
sequence string Protein sequence to analyse. The use of fasta formatted sequence is recommended.

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


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.


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.


Properties of a tool parameter value. Used in wsParameterValue.

Attribute Type Description
key string
value string


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

Attribute Type Description
name string
value list of string


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) Jonassen I, Collins JF, Higgins DG. (1995)
Finding flexible patterns in unaligned protein sequences.
Protein Sci. 4(8):1587-95.
PubMed: 8520485
DOI: 10.1002/pro.5560040817
2) Jonassen I. (1997)
Efficient discovery of conserved patterns using a pattern graph.
Comput Appl Biosci. 13(5):509-22.
PubMed: 9367124
DOI: 10.1093/bioinformatics/13.5.509
services/pfa/pratt_soap.txt · Last modified: 2014/09/05 14:48 by uludag