Workflow Entry: EBI_blastpgp_PSI-BLAST

Created at: 31/05/08 @ 14:39:22

Version 1 (of 1)

Version created on: 31/05/08 @ 14:39:22 by: Hamish McWilliam

Title: EBI_blastpgp_PSI-BLAST

Type: Taverna 1

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Description

Perform a PSI-BLAST iterative search using the EBIâ€™s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

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Workflow Components

Inputs (3)

Name	Description
Sequence_or_ID	Query sequence. Either the actual sequence or an entry identifier in the format database:identifier (e.g. uniprot:wap_rat).
Email_address	User e-mail address.
Search_database	Database to search (e.g. swissprot).

Processors (10)

Name	Type	Description
runBlastpgp	arbitrarywsdl	Submit a PSI-BLAST or PHI-BLAST analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp#runblastpgp_params_content) See the Service entry for this web service.
Job_params	local
Contents_list	local
Get_text_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp#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/blastpgp#poll_jobid_type) See the Service entry for this web service.
Unpack_text_result	local
Unpack_XML_result	local
Input_data	local
EBI_blastpgp_poll_job	workflow
getIds	arbitrarywsdl	Get the hit identifiers from the analysis result (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp#getids_jobid) See the Service entry for this web service.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done

Outputs (4)

Name	Description
Job_ID	EBI job identifier.
Text_result	Plain text PSI-BLAST report from the last iteration.
XML_result	XML BLAST report from the last iteration.
Hit_IDs	Identifiers from the hits found in the last iteration.

Links (16)

Source	Sink
Contents_list:output	runBlastpgp:content
Email_address	Job_params:email
Get_XML_result:output	Unpack_XML_result:bytes
Get_text_result:output	Unpack_text_result:bytes
Job_params:output	runBlastpgp:params
Search_database	Job_params:database
Input_data:output	Contents_list:WSArrayofData
Sequence_or_ID	Input_data:content
Unpack_XML_result:string	XML_result
Unpack_text_result:string	Text_result
getIds:result	Hit_IDs
runBlastpgp:jobid	EBI_blastpgp_poll_job:Job_ID
runBlastpgp:jobid	Get_XML_result:jobid
runBlastpgp:jobid	Get_text_result:jobid
runBlastpgp:jobid	getIds:jobid
runBlastpgp:jobid	Job_ID