Workflow Entry: EBI_blastpgp_PSI-BLAST

Created at: 31/05/08 @ 14:39:23

Version 1 (of 1)

Version created on: 31/05/08 @ 14:39:22 by: Hamish McWilliam | Revision comments Expand

Title: EBI_blastpgp_PSI-BLAST

Type: Taverna 1

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Description

Perform a PSI-BLAST iterative search using the EBI’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)
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)
Get_XML_result	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp#poll_jobid_type)
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)

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)

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