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EBIEMBL-EBI Web Servicesservicesmsaclustalw2_rest
Table of Contents

ClustalW2 (REST)

Description

ClustalW2 1) is a fully automatic program for global multiple alignment of DNA or protein sequences. The alignment is progressive and considers sequence redundancy.

Note: the next generation of Clustal multiple sequence alignment: Clustal Omega, is also available (REST and SOAP web services).

For more information see:

Web service registry entries:

Important

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 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 clustalw2_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/clustalw2/parameters/
Parameters none

Response

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/clustalw2/parameters/

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2/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/clustalw2/parameterdetails/matrix.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/clustalw2/run/
POST email User e-mail address. See Why do you need my e-mail address?
title an optional title for the job.
alignment method used for pairwise alignment stage
type input sequence type
output alignment format
outorder order of sequences in the alignment
sequence sequences to align
Fast pairwise alignment parameters
ktup word size
window window size around best diagonals
score score type
topdiags number of best diagonals
pairgap gap penalty
Slow pairwise alignment parameters
pwmatrix protein scoring matrix
pwdnamatrix DNA/RNA scoring matrix
pwgapopen gap creation penalty
pwgapext gap extension penalty
Multiple alignment parameters
matrix protein scoring matrix
dnamatrix DNA/RNA scoring matrix
gapopen gap creation penalty
noendgaps no end gap separation penalty
gapext gap extension penalty
gapdist gap separation penalty
iteration iteration strategy
numiter maximum number of iterations
clustering clustering method used for guide tree

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

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/clustalw2/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/clustalw2/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/clustalw2/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) Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J. and Higgins D.G. (2007)
Clustal W and Clustal X version 2.0.
Bioinformatics 23(21):2947-8
PubMed: 17846036
DOI: 10.1093/bioinformatics/btm404
 
services/msa/clustalw2_rest.txt · Last modified: 2013/04/30 09:52 by hpm
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