EBI_ScanPS

Created: 2008-06-03 05:57:09 Last updated: 2010-12-06 10:37:50

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Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool.

Note: the WSScanPS service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.

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Workflow Components

Inputs (4)

Name	Description
Email_address	User e-mail address.
Sequence_or_ID	Query sequence. Either the actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. uniprot:wap_rat).
Search_database	Protein sequence database to search (e.g. swissprot).
Search_mode	Search mode: 200 (simple) or 202 (affine)

Processors (7)

Name	Type	Description
runScanPS	arbitrarywsdl	Submit a ScanPS analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/scanps#runscanps_params_content)
Contents_list	local	Wrap input data in list.
Input_data	local	Add type information to input sequence.
Job_params	local	Parameters for the ScanPS job.
Get_output	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/scanps#poll_jobid_type)
Unpack_output	local	Unpack the byte[] returned by the service into a string for display.
EBI_ScanPS_poll_job	workflow	Check job status, fails if job not done.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done

Outputs (2)

Name	Description
ScanPS_job_ID	EBI job identifier.
ScanPS_output	ScanPS search report.

Links (12)

Source	Sink
Contents_list:output	runScanPS:content
Email_address	Job_params:email
Input_data:output	Contents_list:WSArrayofData
Search_mode	Job_params:mode
Sequence_or_ID	Input_data:content
Get_output:output	Unpack_output:bytes
Job_params:output	runScanPS:params
Search_database	Job_params:database
runScanPS:jobid	EBI_ScanPS_poll_job:Job_ID
Unpack_output:string	ScanPS_output
runScanPS:jobid	Get_output:jobid
runScanPS:jobid	ScanPS_job_ID

Coordinations (1)

Controller	Target
EBI_ScanPS_poll_job	Get_output

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Hamish McWilliam

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Information Featured In Packs (2)

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EMBL-EBI Web Services (retired)

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Information Statistics

2168 viewings

2231 downloads

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Version History

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EBI_ScanPS

Created by Hamish McWilliam on Tuesday 03 June 2008 05:57:09 (UTC)

Last edited by Hamish McWilliam on Monday 06 December 2010 10:37:50 (UTC)

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