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CENSOR (REST)

Description

CENSOR 1) screens sequences against a reference collection of sequence repeats, “censors” (masks) homologous portions with masking symbols and generates a report classifying all found repeats. CENSOR supports repeat finding and masking in both nucleotide and 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 censor_lwp.pl LWP and XML::Simple

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

WADL

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

Resources

parameters

List parameter names.

Request

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

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/censor/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/censor/parameterdetails/database.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/censor/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
database Repeat database to search.
mode Search sensitivity mode.
translate Enable/disable translation of input sequence.
identity Enable/disable reporting of identical matches only.
showsimple Enable/disable reporting of simple repeats.
maskpseudo Enable/disable masking of pseusogenes.
sequence Nucleotide or 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 parametersetails 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/censor/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/censor/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/censor/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) Kohany, O., Gentles, A.J., Hankus. L. and Jurka, J. (2006)
Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor.
BMC Bioinformatics 7:474; DOI: 10.1186/1471-2105-7-474; PubMed: 17064419
 
services/so/censor_rest.txt · Last modified: 2014/09/07 08:55 by uludag
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