EMBL-EBI Web Services

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====== WU-BLAST (REST) ======

===== Description =====

WU-BLAST (Washington University Basic Local Alignment Search Tool) Version 2.0 ((Lopez R., Silventoinen V., Robinson S., Kibria A. and Gish W. (2003)\\ 
**WU-Blast2 server at the European Bioinformatics Institute.**\\ 
Nucleic Acids Res. 31(13):3795-8\\ 
PubMed: [[http://europepmc.org/abstract/MED/12824421|12824421]]\\ 
DOI: [[http://dx.doi.org/10.1093/nar/gkg573|10.1093/nar/gkg573]]\\ 
)) is used to compare a sequence with those contained in nucleotide and protein databases by aligning the sequence with previously characterized genes. The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of this novel sequence. Regions of similarity detected via this type of alignment tool can be either local, where the region of similarity is based in 1 location, or global, where regions of similarity can be detected across otherwise unrelated genetic code.

WU-BLAST and NCBI BLAST are distinctly different software packages, although they have a common lineage for some portions of their code, so the services do their work differently, obtain different results and offer different features. 

For more information see:
  * Web form: [[http://www.ebi.ac.uk/Tools/sss/wublast/]]
  * [[.:wu_blast_soap|Document/literal SOAP service]]
  * [[http://blast.wustl.edu/|WU-BLAST website]]

Web service registry entries:
  * [[http://www.programmableweb.com/api/ebi-wu-blast|ProgrammableWeb.com]]

===== Important ====

We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of up to 25 at a time and to not submit more until the results and processing has completed for these. This enables users as well as the service maintainers to deal more easily with local and remote network outages as well as scheduled or unscheduled downtime.

Service provision happens on a fair-share basis. Overzealous usage of a particular resource will be dealt with in accordance to the [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI's Terms of Use]].

===== 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 ^
^ Perl | ''[[http://www.ebi.ac.uk/Tools/webservices/download_clients/perl/lwp/wublast_lwp.pl|wublast_lwp.pl]]'' | [[http://search.cpan.org/perldoc?LWP|LWP]] and [[http://search.cpan.org/perldoc?XML::Simple|XML::Simple]] |

For further details of these tool-kits and workflow platforms see our [[:tutorials:00_Contents|Guide to Web Services]].

===== Resources =====

==== parameters ====

List parameter names.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/parameters/ |
^ Parameters  | //none// |

**Response**

An XML document containing a list of parameter names.

For example: http://www.ebi.ac.uk/Tools/services/rest/wublast/parameters/

==== parameterdetails ====

Get detailed information about a parameter.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/parameterdetails/$parameterId |
^ Parameters  | ''$parameterId'': the name of the parameter |

**Response**

An XML document providing details about the parameter.

For example: http://www.ebi.ac.uk/Tools/services/rest/wublast/parameterdetails/program.

==== run ====

Submit a job with the specified parameters.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/run/ ||
^ POST        | ''email''        | User e-mail address ([[:help:faq#Why do you need my e-mail address?]]). |
^             | ''title''        | An optional title for the job. |
^             | ''program''      | BLAST program to use to perform the search. |
^             | ''matrix''       | Scoring matrix to be used in the search. |
^             | ''alignments''   | Maximum number of alignments displayed in the output. |
^             | ''scores''       | Maximum number of scores displayed in the output. |
^             | ''exp''          | E-value threshold. |
^             | ''filter''       | Low complexity sequence filter to process the query sequence before performing the search. |
^             | ''align''        | Alignment format to use in output. |
^             | ''stats''        | Statistical model to use. |
^             | ''sensitivity''  | Search sensitivity. |
^             | ''topcombon''    | Consistent sets of HSPs to be reported. |
^             | ''viewfilter''   | Display filtered sequence in output. |
^             | ''strand''       | Both, upper or lower strand of a DNA/RNA query used for search. |
^             | ''sort''         | Sort order for reporting hits. |
^             | ''stype''        | Query sequence type. One of: dna, rna or protein. |
^             | ''sequence''     | Query sequence. The use of fasta formatted sequence is recommended. |
^             | ''database''     | List of database names for search. |

More detailed information about each parameter, including valid values can be found in the [[http://www.ebi.ac.uk/Tools/sss/wublast/help/|WU-BLAST help pages]] or obtained using the [[#parameterdetails]] resource.

**Response**

A plain text document containing the job identifier.

==== status ====

Get the status of a submitted job.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/status/$jobId |
^ Parameters  | ''$jobId'': job identifier |

**Response**

A plain text document containing the job status.

The values for the status are:
  * ''RUNNING'': the job is currently being processed.
  * ''FINISHED'': job has finished, and the results can then be retrieved.
  * ''ERROR'': an error occurred attempting to get the job status.
  * ''FAILURE'': the job failed.
  * ''NOT_FOUND'': the job cannot be found.
Further details can be found in [[:tutorials:01_intro#jdispatcher|Synchronous and Asynchronous Access: JDispatcher]].

==== resulttypes ====

Get available result types for a finished job.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/resulttypes/$jobId |
^ Parameters  | ''$jobId'': job identifier |

**Response**

An XML document detailing the available result types.

==== result ====

Get the job result of the specified type.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/wublast/result/$jobId/$resultType |
^ Parameters  | ''$jobId'': job identifier |
^             | ''$resultType'': type of result to retrieve. See [[#resulttypes]]. |

**Response**

A document containing the result in the requested format. The MIME type of the returned document is set according to the format.
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