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

• FASTA/FASTX/FASTY/GGSEARCH/GLSEARCH/SSEARCH/TFASTX/TFASTY
  • FASTA (REST)
  • FASTA (SOAP)
• FASTM/FASTF/FASTS
  • FASTM (REST)
  • FASTM (SOAP)

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

FASTA (pronounced FAST-Aye) stands for FAST-All, reflecting the fact that it can be used for a fast protein comparison or a fast nucleotide comparison. This program achieves a high level of sensitivity for similarity searching at high speed. This is achieved by performing optimised searches for local alignments using a substitution matrix. The high speed of this program is achieved by using the observed pattern of word hits to identify potential matches before attempting the more time consuming optimised search. The trade-off between speed and sensitivity is controlled by the ktup parameter, which specifies the size of the word. Increasing the ktup decreases the number of background hits. Not every word hit is investigated but instead initially looks for segment's containing several nearby hits.

For more information see:

• FASTA homepage
• BioCatalogue

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 WSFasta Clients.

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

Submits a FASTA 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).

Get the entry IDs of the hits in the FASTA output.

Arguments:

• jobid the job identifier specifying the job to get the IDs from.

Returns: a string array of entry IDs.

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.

Deprecated. Use runInterProScan(params, content) instead.

Deprecated. Use poll(jobid, type) instead.

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 = ">TestSequence\nASAMPLESEQ\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 EBI Support.