On Monday 28th March 2011 the WSMafft service was decommissioned and replaced by the following services:

• MAFFT (REST)
• MAFFT (SOAP)

The service documentation and clients below are historical and provided solely for reference purposes.

MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.

For more information about this tool see:

• MAFFT website

Web services registry entries:

• BioCatalogue
• seekda!

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.

For further details see WSMafft Clients.

In addition to these sample clients users have submitted workflows using these services to the myExperiment workflow repository. See workflows using the WSMafft Web Service for a list.

http://www.ebi.ac.uk/Tools/webservices/wsdl/WSMafft.wsdl

Submits a MAFFT job to the service.

Arguments:

• params an instance of the inputParams data structure.
• content a list of data data structures describing the query sequence data.

Returns: a string containing the job ID (jobid).

Arguments:

• sequences string containing the set of sequences to align
• alignment string containing the type of alignment to perform
• email string containing a valid e-mail address.

Returns: a string containing the job ID (jobid).

Arguments:

• database string containing the database name for the set of IDs
• sequences string containing a list of entry IDs
• alignment string containing the type of alignment to perform
• email string containing a valid e-mail address.

Returns: a string containing the job ID (jobid).

Get the status of a job.

Arguments:

• jobid the job identifier of the job to check status of.

Returns: a string indicating the status of the job. Current values are:

• DONE: job has finished, and the results can then be retrieved.
• ERROR: the job failed or no results where found
• NOT_FOUND: the job id is no longer available (job results are deleted after 24 h)
• PENDING: the job is in a queue waiting processing
• RUNNING: the job is currently being processed

Get details of the result types available.

Arguments:

• jobid the job identifier of the job to get result types for.

Returns: an array of WSFile structures describing the available result types for the job.

Wait until the job has finished and get the specified type of result data.

Arguments:

• jobid the job identifier of the job to get result from.
• type a string specifying the type of result to retrieve. See getResults(jobid) and WSFile for details of how to obtain valid values.

Returns: a base64 encoded string containing the result data. Depending on the SOAP library and programming language used the result may be returned in decoded form.

Structure containing the input data for the job

For example to specify an input sequence in Java:

Data inSeq = new Data();
inSeq.setType = "sequence";
inSeq.setContent = ">TestSeq1\nASAMPLESEQ\n" + ">TestSeq2\nANTHERSAMPLESEQ\n" + ">TestSeq3\nYETANTHERSAMPLESEQ\n";

A structure containing the parameters required to run the job.

Structure describing a result type. Returned by the getResults(jobid) method.

If you have any questions or comments, or you plan to use this service as part of a course or for a high number of submissions, please contact us EMBL-EBI Support.