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Pratt (REST)

Description

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

For more information see:

Important

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.

Clients

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
Perl pratt_lwp.pl LWP and XML::Simple

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

Resources

parameters

List parameter names.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/pratt/parameters/

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/$parameterId
Parameters $parameterId: the name of the parameter

Response

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/pratt/parameterdetails/minPerc.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
minPerc Minimum percentage of input sequences to match
patternPosition Pattern position in sequence
maxPatternLength Max pattern length
maxNumPatternSymbols Maximum number Of pattern symbols
maxNumWildcard Maximum length of a widecard (x)
maxNumFlexSpaces Maximum length of flexible spaces
maxFlexibility Maximum flexibility
maxFlexProduct Maximum flex. product
patternSymbolFile Pattern symbol file
numPatternSymbols Number of pattern symbols used in the initial search
patternScoring Pattern scoring
patternGraph Pattern graph allows the use of an alignment or a query sequence to restrict the pattern search
searchGreediness Greediness of the search
patternRefinement Pattern refinemen
genAmbigSymbols Generalise ambiguous symbols
patternFormat PROSITE pattern format
maxNumPatterns Maximum number of patterns
maxNumAlignments Maximum number of alignments between 1 and 100
printPatterns Print Patterns in sequences
printingRatio Printing ratio
printVertically Print vertically
stype input sequence type
sequence 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 parameterdetails resource.

Response

A plain text document containing the job identifier.

status

Get the status of a submitted job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/status/$jobId
Parameters $jobId: job identifier

Response

A plain text document containing the job 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.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/resulttypes/$jobId
Parameters $jobId: job identifier

Response

An XML document detailing the available result types.

result

Get the job result of the specified type.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/pratt/result/$jobId/$resultType
Parameters $jobId: job identifier
$resultType: type of result to retrieve. See resulttypes.

Response

A document containing the result in the requested format. The MIME type of the returned document is set according to the format.

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_rest.txt · Last modified: 2013/10/09 13:55 by hpm
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