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DbClustal (REST)

Description

DbClustal 1) is a ClustalW based alignment workflow for sequences identified by a protein BLAST (NCBI BLAST or WU-BLAST) search. Unlike MView (MView (REST) or MView (SOAP)) the multiple sequence alignment created by DbClustal has the complete sequence of the hits found by BLAST, but with anchor regions in the alignment identified from the BLAST report maintained in the alignment.

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.

Retirement notice: DbClustal will be retired from service in August 2015. If you have any questions/concerns please contact the helpdesk.

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 dbclustal_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 DbClustal (REST) service: http://www.ebi.ac.uk/Tools/services/rest/dbclustal?wadl

Resources

parameters

List parameter names.

Request

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

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dbclustal/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/dbclustal/parameterdetails/output.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/dbclustal/run/
POST email User e-mail address (Why do you need my e-mail address?).
title An optional title for the job.
output Output format for the multiple sequence alignment.
sequence Input query sequence used in the BLAST. For BLAST jobs run on the EMBL-EBI services an EMBL-EBI job identifier can be used as input.
blastreport Input BLAST report from a BLAST search with the query sequence. For BLAST jobs run on the EMBL-EBI services an EMBL-EBI job identifier can be used as input.
idlist Optional list of identifiers for selecting a set of BLAST hits for alignment.

More detailed information about each parameter, including valid values can be found in the DbClustal help pages or 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/dbclustal/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/dbclustal/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/dbclustal/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) Thompson J.D., Plewniak F., Thierry J. and Poch O. (2000)
DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.
Nucleic Acids Research 28(15):2919-26
PubMed: 10908355
DOI: 10.1093/nar/28.15.2919
 
services/msa/dbclustal_rest.txt · Last modified: 2015/02/27 10:17 by apc
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