EMBL-EBI Web Services

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====== DbClustal (REST) ======

===== Description =====

DbClustal ((Thompson J.D., Plewniak F., Thierry J. and Poch O. (2000)\\
**DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches.**\\
Nucleic Acids Research 28(15):2919-26\\ 
PubMed: [[http://europepmc.org/abstract/MED/10908355|10908355]]\\ 
DOI: [[http://dx.doi.org/10.1093/nar/28.15.2919|10.1093/nar/28.15.2919]]\\ 
)) is a ClustalW based alignment workflow for sequences identified by a protein BLAST (NCBI BLAST or WU-BLAST) search. Unlike MView ([[MView (REST)]] or [[MView (SOAP)]]) the multiple sequence alignment created by DbClustal has the complete sequence of the hits found by BLAST, but with anchor regions in the alignment identified from the BLAST report maintained in the alignment.

For more information see:
  * Web form: [[http://www.ebi.ac.uk/Tools/msa/dbclustal/]]
  * [[.:DbClustal (SOAP)|Document/literal SOAP service]]
  * [[ftp://ftp-igbmc.u-strasbg.fr/pub/DbClustal/|DbClustal FTP site]]

===== 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/dbclustal_lwp.pl|dbclustal_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/dbclustal/parameters/ |
^ Parameters  | //none// |

**Response**

An XML document containing a list of parameter names.

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

==== parameterdetails ====

Get detailed information about a parameter.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/dbclustal/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/dbclustal/parameterdetails/output.

==== run ====

Submit a job with the specified parameters.

**Request**

^ URL         | http://www.ebi.ac.uk/Tools/services/rest/dbclustal/run/ ||
^ POST        | ''email''        | User e-mail address ([[:help:faq#Why do you need my e-mail address?]]). |
^             | ''title''        | An optional title for the job. |
^             | ''output''    | Output format for the multiple sequence alignment. |
^             | ''sequence''     | Input query sequence used in the BLAST. For BLAST jobs run on the EMBL-EBI services an EMBL-EBI job identifier can be used as input. |
^             | ''blastreport''  | Input BLAST report from a BLAST search with the query sequence. For BLAST jobs run on the EMBL-EBI services an EMBL-EBI job identifier can be used as input. |
^             | ''idlist'' | Optional list of identifiers for selecting a set of BLAST hits for alignment. |

More detailed information about each parameter, including valid values can be found in the [[http://www.ebi.ac.uk/Tools/msa/dbclustal/help/|DbClustal 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/dbclustal/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/dbclustal/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/dbclustal/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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