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EBIEBI Web Servicesservicesmsakalign_rest

Kalign (REST)

Description

A fast and accurate multiple sequence alignment algorithm.

For more information see:

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 kalign_lwp.pl LWP and XML::Simple

Resources

parameters

List parameter names.

Request

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

Response

An XML document containing a list of parameter names.

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

parameterdetails

Get detailed information about a parameter.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/kalign/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/kalign/parameterdetails/format.

run

Submit a job with the specified parameters.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/kalign/run/
POST email User e-mail address.
title an optional title for the job.
stype sequence type.
format output alignment format.
gapopen gap creation penalty.
gapext gap extension penalty.
termgap terminal gap penalty.
bonus bonus score.
sequence input sequences.

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/kalign/status/$jobId
Parameters $jobId: job identifier

Response

A plain text document containing the job status.

resulttypes

Get available result types for a finished job.

Request

URL http://www.ebi.ac.uk/Tools/services/rest/kalign/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/kalign/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.

 
services/msa/kalign_rest.txt · Last modified: 2009/12/14 10:49 (external edit)
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