Table of Contents
On Monday 28th March 2011 the WSTCoffee service was decommissioned and replaced by the following services:
The service documentation and clients below are historical and provided solely for reference purposes.
T-Coffee is a multiple sequence alignment program. Multiple sequence alignment programs are meant to align a set of sequences previously gathered using other programs such as BLAST or FASTA. The main characteristic of T-Coffee is that it will allow you to combine results obtained with several alignment methods. For instance if you have an alignment coming from ClustalW, an other alignment coming from Dialign, and a structural alignment of some of your sequences, T-Coffee will combine all that information and produce a new multiple sequence having the best agreement with all these methods. By default, T-Coffee will compare all your sequences two by two, producing a global alignment and a series of local alignments (using lalign). The program will then combine all these alignments into a multiple alignment.
For more information about this tool see:
Web services registry entries:
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 WSTCoffee Clients.
Submits a T-Coffee job to the service.
Returns: a string containing the job ID (
Get the status of a job.
Returns: a string indicating the status of the job. Current values are:
Get details of the result types available.
Returns: an array of
Wait until the job has finished and get the specified type of result data.
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
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.