EMBL-EBI Web Services

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====== WSNCBIBlast ======

===== Important =====

On Monday 28th March 2011 the WSNCBIBlast service was **decommissioned** and replaced by the following services:
  * [[:services:sss:NCBI BLAST (REST)]]
  * [[:services:sss:NCBI BLAST (SOAP)]]

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

===== Description =====

NCBI BLAST is a sequence similarity search program. The emphasis is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of the query sequence. [[.:wswublast|WU-BLAST]] and NCBI BLAST are distinctly different software packages, although they have a common lineage for some portions of their code, so the two services do their work differently, obtain different results and offer different features. 

For more information about this tool see:
  * 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 services registry entries:
  * [[http://www.biocatalogue.org/services/44|BioCatalogue]]
  * [[http://webservices.seekda.com/providers/ebi.ac.uk/WSNCBIBlastService|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/wsncbiblast.exe|wsncbiblast.exe]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/csharp/src/wsncbiblast.cs|wsncbiblast.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/WSNCBIBlast.jar|WSNCBIBlast.jar]]''; Source: ''[[http://www.ebi.ac.uk/Tools/webservices/downloads/java/src/uk/ac/ebi/webservices/WSNCBIBlastClient.java|WSNCBIBlastClient.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/ncbiblast.pl|ncbiblast.pl]]'' | [[http://search.cpan.org/perldoc?SOAP::Lite|SOAP::Lite]] |
^ Taverna 1.x | [[http://www.myexperiment.org/workflows/201|EBI_NCBI_BLAST]] | [[http://www.taverna.org.uk/|Taverna]] |

For further details see [[.:WSNCBIBlast 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%2FWSNCBIBlast.wsdl"%29|workflows using the WSNCBIBlast Web Service]] for a list.

===== WSDL =====

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

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

==== runNCBIBlast(params, content) ====

Submits a NCBI 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 ^ 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** |

For example to specify an input [[http://www.ebi.ac.uk/blastall/blastall_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 ^ Description ^ Default ^
| **[[http://www.ebi.ac.uk/Tools/blastall/help.html#program|program]]** | string | BLAST program to use. Valid values are: 'blastn', 'blastp', 'blastx' | **required** |
| **[[http://www.ebi.ac.uk/Tools/blastall/help.html#database|database]]** | string | Database to search. See [[help:databases#similarity_homology_search_databases|databases]] | **required** |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#matrix|matrix]] | string | Scoring matrix to use. See [[help::matrix]] | BLOSUM62 |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#alignments|numal]] | integer | Maximum number of alignments to output | 50 |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#scores|scores]] | integer | Maximum number of scores to output | 100 |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#expthr|exp]] | float | Statistical significance threshold | 10 |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#filter|filter]] | boolean | Mask low complexity sequence | false|
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#OPENGAP|opengap]] | integer | Gap open penalty | |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#EXTENDGAP|extendgap]] | integer | Gap extension penalty | |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#DROPOFF|dropoff]] | integer | Drop-off | |
| [[http://www.ebi.ac.uk/Tools/blastall/help.html#GAPALIGN|gapalign]] | boolean | Perform optimised alignments within regions involving gaps | true |
| match        | integer | Reward for a nucleotide match (blastn only)     | |
| mismatch     | integer | Penalty for a nucleotide mismatch (blastn only) | |
| async        | boolean | Asynchronous submission (recommended) | 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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