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Introduction

Pratt - Pattern Matching. An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to search for patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.

Official Website

Pratt website

Download Software

FTP Download

Important Note

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

How to Access Pratt

Pratt can be accessed via

Web Form

Web interface for Pratt is available at : https://www.ebi.ac.uk/Tools/pfa/pratt/

How to use this tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Input Sequences

Input Sequence

The input set of up to 100 sequences can be entered directly into this form. The sequences can be in FASTA or UniProtKB/Swiss-Prot format. Partially formatted sequences are not accepted. (See example input formats). Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing up to 100 valid sequences in FASTA or UniProtKB/Swiss-Prot format can be used as input. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present. It is best to save files with the Unix format option to avoid hidden Windows characters.

Step 2 - Set alignment options

minPerc

Set the minimum percentage of the input sequences that should match a pattern (C%). If you set this to, say 80, Pratt will only report patterns matching at least 80 % of the sequences input.

Default value is: 100

Pattern Position

Pattern position in sequence (PP parameter)

Pattern PositionAbbreviation
offoff
completecomplete
startstart

Default value is: off

Max Pattern Length

Maximum pattern length (PL parameter) allows you to set the maximum length of a pattern. The length of the pattern C-x(2,4)-[DE] is 1+4+1=6. The memory requirement of Pratt depends on L; a higher L value gives higher memory requirement.

Default value is: 50

Max Num Pattern Symbols

Maximum number of pattern symbols (PN parameter). Using this you can set the maximum number of symbols in a pattern. The pattern C-x(2,4)-[DE] has 2 symbols (C and [DE]). When PN is increased, Pratt will require more memory.

Default value is: 50

Max Num Wildcard

Maximum length of a widecard (x). Using this option you can set the maximum length of a wildcard (PX parameter). Increasing this will increase the time used by Pratt, and also slightly the memory required.

Default value is: 5

Max Num Flex Spaces

Maximum length of flexible spaces. Using this option you can set the maximum number of flexible wildcards (matching a variable number of arbitrary sequence symbols) (FN parameter). Increasing this will increase the time used by Pratt.

Default value is: 2

Max Flexibility

Maximum flexibility. You can set the maximum flexibility of a flexible wildcard (matching a variable number of arbitrary sequence symbols) (FL parameter). For instance x(2,4) and x(10,12) has flexibility 2, and x(10) has flexibility 0. Increasing this will increase the time used by Pratt.

Default value is: 2

Max Flex Product

Maximum flex. product. Using this option you can set an upper limit on the product of a flexibilities for a pattern (FP parameter). This is related to the memory requirements of the search, and increasing the limit, increases the memory usage.

Default value is: 10

Pattern Symbol File

Pattern Symbol File (BI parameter)

Default value is: Off [false]

Num Pattern Symbols

Number of pattern symbols used in the initial search (BN parameter).

Default value is: 20

Pattern Restriction File

Pattern restriction file. The restriction file limits the sequence range via the start/end parameter and is in the format ">Sequence (start, end)". If parameter PP is off, the restiction file will be ignored.

Pattern Scoring

Pattern scoring (S parameter)

Pattern ScoringAbbreviation
infoinfo
mdlmdl

Default value is: info

Pattern Graph

Pattern Graph (G parameter) allows the use of an alignment or a query sequence to restrict the pattern search.

Pattern GraphAbbreviation
seqseq

Default value is: seq

Search Greediness

Using the greediness parameter (E) you can adjust the greediness of the search. Setting E to 0 (zero), the search will be exhaustive. Increasing E increases the greediness, and decreases the time used in the search.

Default value is: 3

Pattern Refinement

Pattern Refinement (R parameter). When the R option is switched on, patterns found during the initial pattern search are input to a refinement algorithm where more ambiguous pattern symbols can be added.

Default value is: Off [false]

Gen Ambig Symbols

Generalise ambiguous symbols (RG parameter). If the RG option is switched on, then ambiguous symbols listed in the symbols file are used. If RG is off, only the letters needed to match the input sequences are included in the ambiguous pattern positions.

Default value is: Off [false]

Pattern Format

PROSITE Pattern Format (OP parameter). When switched on, patterns will be output in PROSITE style (for instance C-x(2,4)-[DE]). When switched off, patterns are output in a simpler consensus pattern style (for instance Cxx--[DE] where x matches exactly one arbitrary sequence symbol and - matches zero or one arbitrary sequence symbol).

Default value is: On [true]

Max Num Patterns

Maximum number of patterns (ON parameter) between 1 and 100.

Default value is: 50

Max Num Alignments

Maximum number of alignments (OA parameter) between 1 and 100.

Default value is: 50

Print Patterns

Print Patterns in sequences (M parameter) If the M option is set, then Pratt will print out the location of the sequence segments matching each of the (maximum 52) best patterns. The patterns are given labels A, B,...Z,a,b,...z in order of decreasing pattern score. Each sequence is printed on a line, one character per K-tuple in the sequence. If pattern with label C matches the third K-tuple in a sequence C is printed out. If several patterns match in the same K-tuple, only the best will be printed.

Default value is: On [true]

Printing Ratio

Printing ratio (MR parameter). sets the K value (ratio) used for printing the summary information about where in each sequence the pattern matches are found.

Default value is: 10

Print Vertically

Print vertically (MV parameter). if set, the output is printed vertically instead of horizontally, vertical output can be better for large sequence sets.

Default value is: Off [false]


Example output formats

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form joe@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

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Web Services

Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. 

For an introduction on how to run these clients and use them in workflows please see the webinar series.


REST API

The Representational State Transfer (REST) 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.

LanguageDownloadRequirements
Perlpratt.plLWP and XML::Simple

Python

pratt.py

xmltramp2

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

WADL

The WADL for the Pratt (REST) service: http://www.ebi.ac.uk/Tools/services/rest/pratt?wadl


Parameters

Command line parameter
MIN PERCENTAGE--minPerc
PATTERN POSITION--patternPosition
MAX PATTERN LENGTH--maxPatternLength
MAX NUM PATTERN SYMBOLS--maxNumPatternSymbols
MAX NUM WILDCARD--maxNumWildcard
MAX NUM FLEX SPACES--maxNumFlexSpaces
MAX FLEXIBILITY--maxFlexibility
MAX FLEX PRODUCT--maxFlexProduct
PATTERN SYMBOL FILE--patternSymbolFile
NUM PATTERN SYMBOLS--numPatternSymbols
PATTERN SCORING--patternScoring
PATTERN GRAPH--patternGraph
SEARCH GREEDINESS--searchGreediness
PATTERN REFINEMENT--patternRefinement
GEN AMBIG SYMBOLS--genAmbigSymbols
PATTERN FORMAT--patternFormat
MAX NUM PATTERNS--maxNumPatterns
MAX NUM ALIGNMENTS--maxNumAlignments
PRINT PATTERNS--printPatterns
PRINT RATIO--printingRatio
PRINT VERTICALLY--printVertically

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SOAP API

The Simple Object Access Protocol (SOAP) 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.

WSDL

The WSDL for the Pratt (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/pratt?wsdl


MethodsDescriptionArgumentsReturns

getParameters()

Get a list of the parameter names.nonea list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameter.parameterId: identifier/name of the parameter to fetch details of.a wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service.
  • email: (required) user e-mail address. See Why do you need my e-mail address?

  • title: job title. Default: ””.

  • params: (required) parameters for the tool. These are described by the InputParameters data structure.

a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.jobId: (required) job identifier.

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.

getResultTypes(jobId)

Get the available result types for a finished job.jobId: (required) job identifier.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.

InputParameters

The input parameters for the job:

AttributeTypeDescription
minPercintMinimum percentage of input sequences to match.
patternPositionstringPattern position in sequence.
maxPatternLengthintMax pattern length.
maxNumPatternSymbolsintMaximum number Of pattern symbols.
maxNumWildcardintMaximum length of a widecard (x).
maxNumFlexSpacesintMaximum length of flexible spaces.
maxFlexibilityintMaximum flexibility.
maxFlexProductintMaximum flex. product.
patternSymbolFilebooleanPattern symbol file.
numPatternSymbolsintNumber of pattern symbols used in the initial search.
patternScoringstringPattern scoring.
patternGraphstringPattern graph allows the use of an alignment or a query sequence to restrict the pattern search.
searchGreedinessintthe greediness of the search.
patternRefinementbooleanPattern refinement.
genAmbigSymbolsbooleanGeneralise ambiguous symbols.
patternFormatbooleanPROSITE pattern format.
maxNumPatternsintMaximum number of patterns.
maxNumAlignmentsintMaximum number of alignments between 1 and 100.
printPatternsbooleanPrint Patterns in sequences .
printingRatiointPrinting ratio.
printVerticallybooleanPrint vertically.
stypestringInput sequence type.
sequencestringProtein 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.

wsParameterDetails

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

AttributeTypeDescription
namestringName of the parameter.
descriptionstringDescription of the parameter, suitable for use in option help interfaces.
typestringData type of the parameter.
valueslist of wsParameterValueList of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

AttributeTypeDescription
labelstringDisplay name of the value, for use in interfaces.
valuestringString representation of the value to be passed to the tool parameter.
defaultValuebooleanFlag indicating if this value is the default.
propertieslist of wsPropertyList of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

AttributeTypeDescription
keystringProperty name
valuestringProperty value

wsRawOutputParameter

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

AttributeTypeDescription
namestringParameter name
valuelist of stringParameter value

wsResultType

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

AttributeTypeDescription
identifierstringIdentifier for the result type. Passed as type to getResult(jobId, type, parameters).
labelstringDisplay name for use in user interfaces.
descriptionstringDescription of the result type, for use in help interfaces.
mediaTypestringMIME type of the returned data.
fileSuffixstringSuggested suffix for file name, if writing data to disk.

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Open API Interface

https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=pratt


Endpoints

DescriptionArgumentsReturns

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameters

Get a list of the parameter names.noneA list of strings giving the names of the parameters.

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/minPerc

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternPosition

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxPatternLength

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxNumPatternSymbols

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxNumWildcard

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxNumFlexSpaces

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxFlexibility

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxFlexProduct

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternSymbolFile

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/numPatternSymbols

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternScoring

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternGraph

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/searchGreediness

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternRefinement

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/genAmbigSymbols

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/patternFormat

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxNumPatterns

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/maxNumAlignments

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/printPatterns

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/printingRatio

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/printVertically

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/stype

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/sequence

https://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/ppfile

Get details of a specific parameter.parameterdetail: identifier/name of the parameter to fetch details of.A wsParameterDetails describing the parameter and its values.

https://www.ebi.ac.uk/Tools/services/rest/pratt/run

Submit a job to the service.

email: (required) user e-mail address. See Why do you need my e-mail address?

title: job title. Default: ””.

params: (required) parameters for the tool. These are described by the InputParameters data structure.

A string containing the job identifier (jobId).

https://www.ebi.ac.uk/Tools/services/rest/pratt/status/<jobid>

Get the status of a submitted job.jobId: (required) job identifier.

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: Job Dispatcher.

https://www.ebi.ac.uk/Tools/services/rest/pratt/resulttypes/<jobid>

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.

https://www.ebi.ac.uk/Tools/services/rest/pratt/result/<jobid>/out

https://www.ebi.ac.uk/Tools/services/rest/pratt/result/<jobid>/stdout

https://www.ebi.ac.uk/Tools/services/rest/pratt/result/<jobid>/error

https://www.ebi.ac.uk/Tools/services/rest/pratt/result/<jobid>/sequence

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.

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Common Workflow Language

CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl

For details, see CWL Workflows page. 

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Reference 

Pratt

EBI  Web Services

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