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EBI_NCBI_BLAST

Workflow Entry: EBI_NCBI_BLAST

Created at: 31/05/08 @ 08:38:46 Last updated: 06/12/10 @ 10:54:16

Version 1 (of 1)

Version created on: 31/05/08 @ 08:38:46 by: Hamish McWilliam

Last edited on: 06/12/10 @ 10:54:16 by: Hamish McWilliam

Title: EBI_NCBI_BLAST

Type: Taverna 1

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Description

Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default.

Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLAST services (REST or SOAP) should be used instead.

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http://www.myexperiment.org/workflows/201/download?version=1
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Workflow Components

Inputs (4)

Name	Description
Sequence_or_ID	Query seqeunce. Either the actual sequence (fasta format recommended) or a database identifer in database:identifier format (e.g. uniprot:wap_rat).
Search_database	The database to search (e.g. uniprot).
BLAST_program	The BLAST program to use for the search (e.g. blastn, blastp or blastx).
Email_address	Your e-mail address.

Processors (10)

Name	Type	Description
runNCBIBlast	arbitrarywsdl	Submit a NCBI BLAST analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#runncbiblast_params_content) See the Service entry for this web service.
Job_params	local	Parameters for the NCBI BLAST job.
Content_list	local	Wrap the input data in a list.
Input_data	local	Add a type to the input sequence/identifer.
EBI_NCBI_BLAST_job_poll	workflow	Check if job has completed.
getIds	arbitrarywsdl	Get the hit identifiers from the analysis result (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#getids_jobid) See the Service entry for this web service.
Get_text_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type) See the Service entry for this web service.
Get_XML_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type) See the Service entry for this web service.
Unpack_text_result	local	Covert byte[] to string for plain text BLAST output.
Unpack_XML_result	local	Covert byte[] to string for XML BLAST output.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done	Convert job status to true/false.	job_status	is_done

Outputs (4)

Name	Description
Job_ID	Identifer fot the job at EBI.
Text_result	The BLAST report output in plain text.
XML_result	The BLAST report output in XML.
Hit_ID_List	List of identifiers of the hits.

Links (17)

Source	Sink
BLAST_program	Job_params:program
Content_list:output	runNCBIBlast:content
Email_address	Job_params:email
Get_XML_result:output	Unpack_XML_result:bytes
Get_text_result:output	Unpack_text_result:bytes
Input_data:output	Content_list:WSArrayofData
Job_params:output	runNCBIBlast:params
Search_database	Job_params:database
Sequence_or_ID	Input_data:content
Unpack_XML_result:string	XML_result
Unpack_text_result:string	Text_result
runNCBIBlast:jobid	EBI_NCBI_BLAST_job_poll:Job_ID
runNCBIBlast:jobid	Get_XML_result:jobid
runNCBIBlast:jobid	Get_text_result:jobid
getIds:result	Hit_ID_List
runNCBIBlast:jobid	getIds:jobid
runNCBIBlast:jobid	Job_ID

Coordinations (3)

Controller	Target
EBI_NCBI_BLAST_job_poll	getIds
EBI_NCBI_BLAST_job_poll	Get_text_result
EBI_NCBI_BLAST_job_poll	Get_XML_result

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

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Hamish McWilliam

Information Attributions (0)

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Information Tags (6)

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Information Featured In Packs (2)

Private pack
EMBL-EBI Web Services (retired)

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Information Attributed By (6)

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Information Statistics

1934 viewings

1431 downloads

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Citations (0)

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Version History

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EBI_NCBI_BLAST

Created by Hamish McWilliam on Saturday 31 May 2008 @ 08:38:46 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 @ 10:54:16 (UTC)

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Comments (1)

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Paul Fisher

After contacting the author, I was directed to:

http://www.ebi.ac.uk/Tools/webservices/help/databases#similarity_homology_search_databases

This URL contains information on the databases to use in your search.

regards,

Paul.

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Created: 03/10/07 @ 18:36:22

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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Viewed: 284 times | Downloaded: 112 times

Tags (3):

Taverna 1

Original Uploader

Hamish McWilliam

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EBI_NCBI_BLAST_with_prompts (1)

Created: 31/05/08 @ 08:40:29 | Last updated: 06/12/10 @ 10:55:09

Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST

License: Creative Commons Attribution 3.0 Unported License

Run a BLAST analysis using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...