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Table of Contents
T-Coffee (SOAP)DescriptionT-Coffee 1) 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 see:
Web service registry entries: ImportantWe 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. ClientsSample 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 of these tool-kits and workflow platforms see our Guide to Web Services. WSDLThe WSDL for the T-Coffee SOAP service: http://www.ebi.ac.uk/Tools/services/soap/tcoffee?wsdl The Kissinger Research Group, University of Georgia provide a SAWSDL for the T-Coffee (SOAP) web service, which is annotated using OBIws: http://mango.ctegd.uga.edu/jkissingLab/SWS/Wsannotation/resources/tcoffee.sawsdl OperationsgetParameters()Get a list of the parameter names. Arguments: none Returns: a list of strings giving the names of the parameters. getParameterDetails(parameterId)Get details of a specific parameter. Arguments:
Returns: a wsParameterDetails describing the parameter and its values. run(email, title, params)Submit a job to the service. Arguments:
Returns: a string containing the job identifier ( getStatus(jobId)Get the status of a submitted job. Arguments:
Returns: a string containing the status. The values for the status are:
Further details can be found in Synchronous and Asynchronous Access: JDispatcher. getResultTypes(jobId)Get the available result types for a finished job. Arguments:
Returns: a list of wsResultType data structures describing the available result types. getResult(jobId, type, parameters)Get the result of a job of the specified type. Arguments:
Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string. Data TypesInputParametersThe input parameters for the job:
More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation. wsParameterDetailsDescriptive information about a tool parameter. Returned by getParameterDetails(parameterId).
wsParameterValueDescription of a tool parameter value. Used in wsParameterDetails.
wsPropertyProperties of a tool parameter value. Used in wsParameterValue.
wsRawOutputParameterAdditional parameters passed when requesting a result. See getResult(jobId, type, parameters).
wsResultTypeDescription of a result type. Returned by getResultTypes(jobId).
1)
Notredame C., Higgins D.G. and Heringa J. (2000)
T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology 302(1):205-17 PubMed: 10964570 DOI: 10.1006/jmbi.2000.4042 | |
