EMBL-EBI Web Services

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====== WSBlastpgp ======

===== Important =====

On Monday 28th March 2011 the WSBlastpgp service was **decommissioned** and replaced by the following services:
  * [[:services:sss:psiblast_rest|PSI-BLAST (REST)]]
  * [[:services:sss:psiblast_soap|PSI-BLAST (SOAP)]]

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

===== Description =====

Position Specific Iterative BLAST (PSI-BLAST) performs an iterative sequence similarity search which can detect more distant evolutionary relationships.

Pattern Hit Initiated BLAST (PHI-BLAST) treats multiple occurrences of a defined pattern within the query sequence as independent sequences.

These tools are only available for database protein searches.

The iterative strategy of PSI-BLAST can be run in two ways:
  - Manual: at each iteration the list of hits found is returned and the hits used to generate the profile the next iteration are selected and submitted to perform the nest iteration.
  - Automatic: the set of hits used to construct the profile is automatically selected based on an E-value threshold. For this mode the search will stop either when the iterations converge (i.e. the same hits are used to build the profile in each iteration) or when a specified maximum number of iterations is reached.

This service provides only the automatic mode. To use the manual mode see the [[.:WSPSIBlast]], [[:services:sss:psiblast_soap|PSI-BLAST (SOAP)]] or [[:services:sss:psiblast_rest|PSI-BLAST (REST)]] services.

For more information on this tool see:
  * EMBL-EBI Tools:
    * [[http://www.ebi.ac.uk/Tools/blastpgp/|PSI-BLAST/PHI-BLAST]]
    * [[http://www.ebi.ac.uk/Tools/blastpgp/help.html|PSI-BLAST/PHI-BLAST Help]]
  * NCBI:
    * [[http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs|NCBI BLAST Help]]
    * [[http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/guide.html|BLAST Guide]]

Web service registry entries:
  * [[http://www.biocatalogue.org/services/2048|BioCatalogue]]
  * [[http://webservices.seekda.com/providers/ebi.ac.uk/WSBlastpgpService|seekda!]]

===== Clients =====

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 ^
^ C# | .NET Executable: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/bin/wsblastpgp.exe|wsblastpgp.exe]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/src/wsblastpgp.cs|wsblastpgp.cs]]'' | A .NET runtime environment. If building from source development tools are also required. See the [[tutorials:06_Programming:dot_net|.NET tutorial]] for details. |
^ Java | Executable jar: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/bin/WSBlastpgp.jar|WSBlastpgp.jar]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/src/uk/ac/ebi/webservices/WSBlastpgpClient.java|WSBlastpgpClient.java]]'' | [[http://ws.apache.org/axis/|Axis 1.4]]; All dependencies, including [[http://ws.apache.org/axis/|Axis 1.4]] and [[http://commons.apache.org/cli/|Commons-CLI]], are available in ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/lib-1.4.zip|lib-1.4.zip]]''. |
^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/perl/soaplite/blastpgp.pl|blastpgp.pl]]'' | [[http://search.cpan.org/perldoc?SOAP::Lite|SOAP::Lite]] |
^ Taverna 1.x | [[http://www.myexperiment.org/workflows/208|EBI_blastpgp_PSI-BLAST]] | [[http://www.taverna.org.uk/|Taverna]] |

For further details see [[WSBlastpgp Clients]].

==== Workflows ====

In addition to these sample clients users have submitted workflows using these services to the [[http://www.myexperiment.org/|myExperiment]] workflow repository. See [[http://www.myexperiment.org/workflows?filter=WSDL_ENDPOINT%28"http%3A%2F%2Fwww.ebi.ac.uk%2FTools%2Fwebservices%2Fwsdl%2FWSBlastpgp.wsdl"%29|workflows using the WSBlastpgp Web Service]] for a list.

===== WSDL =====

WSDL service description:

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

===== Service API =====

==== runBlastpgp(params, content) ====

Submits a PSI-BLAST/PHI-BLAST job to the service.

Arguments:
  * ''params'' an instance of the ''[[#inputParams|inputParams]]'' data structure.
  * ''content'' a list of ''[[#data|data]]'' data structures describing the query sequence data. 

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

==== getIds(jobid) ====

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

Arguments:
  * ''jobid'' the job identifier specifying the job to get the IDs from.

Returns: a string array of entry IDs.
==== checkStatus(jobId) ====

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

==== getResults(jobid) ====

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|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.

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|getResults(jobid)]] and [[#WSFile|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.

==== data ====

Structure containing the input data for the job

^ Attribute    ^ Type   ^ Values                                               ^ Default ^
| **type** | string | ''sequence'', ''dbfetch'' | **required** |
| **content** | string  | db:id identifier or formatted sequence | **required** |

For example to specify an input [[http://www.ebi.ac.uk/blastpgp/blastpsi_wsequence_frame.html|sequence]] in Java:
<code java>
Data inSeq = new Data();
inSeq.setType = "sequence";
inSeq.setContent = ">TestSequence\nASAMPLESEQ\n";
</code>
==== inputParams ====

A structure containing the parameters required to run the job.

^ Attribute    ^ Type   ^ Values                                               ^ Default ^
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#program|mode]] | string | 'PSI-Blast' or 'PHI-Blast' | **required** |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#database|database]] | string | see [[help::databases#similarity_homology_search_databases|databases]] | **required** |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#matrix|matrix]] | string | [[help:matrix|scoring matrix name]] | BLOSUM62 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#expthr|exp]] | float | 1.0e-200 < exp < 1000 | 10.0 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#expthr_multi|expmulti]] | float | 0.0001 < expmulti < 1000 | 0.002 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#filter|filter]] | string | T (true) or F (false) | F |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#align|align]] | int | 0 (pairwise), 1 (M/S identities), 2 (M/S non-identities), 3 (Flat identities), 4 (Flat non-identities) | 0 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#OPENGAP|opengap]] | int | | 11 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#EXTENDGAP|extendgap]] | int | | 1 |
| gapalign | string | //not used// | |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#DROPOFF|dropoff]] | int | | 15 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#FINALDROPOFF|finaldropoff]] | int | | 25 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#MAXPASSES|maxpasses]] | int | | 3 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#scores|scores]] | int | | 500 |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#seqrange|startregion]] | int | | whole sequence |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#seqrange|endregion]] | int | | whole sequence|
| sensitivity | string | //not used// | |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#format|appxml]] | string | no (text) or yes (XML) | no |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#USAGEMODE|usagemode]] | string | blastpgp, patseedp or seedp | blastpgp |
| [[http://www.ebi.ac.uk/Tools/blastpgp/help.html#UPLOADAPATTERNFILE|pattern]] | string | | |
| async        | boolean | true or false | false |
| **email**    | string  | Valid email address. See [[help:faq#why_do_you_need_my_e-mail_address|Why do you need my e-mail address?]] | **required** |

==== WSFile ====

Structure describing a result type. Returned by the ''[[#getResults_jobid|getResults(jobid)]]'' method.

^ Attribute ^ Type   ^ Description |
| **type**  | string | Symbolic name of the result type. Used with the ''[[#poll_jobid_type|poll(jobid, type)]]'' method. |
| **ext**   | string | Recommended file extension for this result type. |

===== Contact =====

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 [[http://www.ebi.ac.uk/support/index.php?query=WebServices|EMBL-EBI Support]].
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