Table of Contents
On Monday 28th March 2011 the WSFasta service was decommissioned and replaced by the following services:
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:
Web service 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 WSFasta Clients.
Submits a FASTA job to the service.
Returns: a string containing the job ID (
Get the entry IDs of the hits in the FASTA output.
Returns: a string array of entry IDs.
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 = ">TestSequence\nASAMPLESEQ\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.