Workflow Entry: EBI_NCBI_BLAST

Created at: 31/05/08 @ 08:38:49 Last updated: 02/06/08 @ 21:32:22

Version 1 (of 1)

Version created on: 31/05/08 @ 08:38:46 by: Hamish McWilliam | Revision comments Expand

Last edited on: 02/06/08 @ 21:32:21 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.

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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)
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)
Get_text_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type)
Get_XML_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast#poll_jobid_type)
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)

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