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

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


PSI-Search, similar to PSI-BLAST, combines the Smith-Waterman search algorithm with the PSI-BLAST profile construction strategy to find distantly related protein sequences. Searches are done with SSEARCH, and the selected hits are combined with BLASTPGP to build a position specific scoring matrix (PSSM), which is then used for another search with SSEARCH in the next iteration.

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.

Language Download Requirements
Perl SOAP::Lite

For further details see WSPSISearch Clients.


Service API

runPSISearch(params, content, preselseqcontent, checkpointcontent)

Submits a PSI-Search job to the service.


  • params an instance of the inputParams data structure.
  • content data data structures describing the query sequence data.
  • preselseqcontent data structures describing the pre-selelcted sequence data.
  • checkpointcontent data structures describing the checkpoint data.

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


Get the status of a job.


  • 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.


  • 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.

poll(jobid, type)

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


  • 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

Attribute Type Description Default
type string Type of content being used. Valid values are: 'sequence' and 'dbfetch' required
content string A sequence entry identifier in db:id format or a formatted sequence (fasta recommended) required
preselseqcontent file A sequence file containing pre-selected sequences for next iteration optional
checkpointcontent file A checkpoint file for next iteration optional


A structure containing the parameters required to run the job.

Attribute Type Description Default
database string The subject database for searching required
matrix string Scoring matrix blosum62
exp real E-value (0<E⇐ 1000). Statistical significance threshold for reporting database sequence matches. 10
expmulti real PSI-Search threshold (0<E⇐ 1000). Statistical significance threshold for selecting hits for next iteration 0.001
align int number of alignments to be reported 500
scores int number of scores to be reported 500
numal int Number of alignments 500
opengap int Gap open penalty 11
extendgap int Gap extension penalty 1
checkpoint file checkpoint file for further iteration Optional
preselseq file selected sequences for next iteration Optional
async boolean Asynchronous submission false
email string Valid email address. See Why do you need my e-mail address? required


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

Attribute Type Description
type string Symbolic name of the result type. Used with the poll(jobid, type) method.
ext string Recommended file extension for this result type.


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.

services/archive/sss/wspsisearch.txt · Last modified: 2013/04/23 16:45 by hpm