EBI_CENSOR

Created: 2008-06-17 20:42:46 Last updated: 2008-06-25 06:16:03

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The CENSOR tool identifies and masks simple and complex sequence repeats found in nucleotide and protein sequences. This workflow uses the EBI's WSCensor web service (see http://www.ebi.ac.uk/Tools/webservices/services/censor) to access the tool.

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Workflow Components

Inputs (3)

Name	Description
Email	User e-mail address.
Sequence_or_ID	Input sequence. Either an actual sequence (fasta format recommended) or an entry identifier in database:identifier format (e.g. embl:AJ608703).
Repeat_library	Library of complex repeats to search against (e.g. Fungi).

Processors (11)

Name	Type	Description
Unpack_table	local
Unpack_masked_sequence	local
Unpack_alignment	local
Contents_list	local
Input_data	local
Job_params	local
runCensor	arbitrarywsdl	Submit a CENSOR analysis job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#runcensor_params_content)
Get_alignment	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
Get_table	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
Get_masked_sequence	arbitrarywsdl	Get the results of a job (see http://www.ebi.ac.uk/Tools/webservices/services/censor#poll_jobid_type)
EBI_CENSOR_poll_job	workflow	Check status of a WSCensor job.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done

Outputs (4)

Name	Description
CENSOR_job_ID
CENSOR_masked_sequence	Repeat masked sequence in fasta format.
CENSOR_alignment	Alignments of the repeat signature sequences with the masked regions.
CENSOR_table	Table describing maksed regions and identified repeats.

Links (17)

Source	Sink
Contents_list:output	runCensor:content
Email	Job_params:email
Get_alignment:output	Unpack_alignment:bytes
Get_masked_sequence:output	Unpack_masked_sequence:bytes
Get_table:output	Unpack_table:bytes
Input_data:output	Contents_list:WSArrayofData
Job_params:output	runCensor:params
Repeat_library	Job_params:lib
Sequence_or_ID	Input_data:content
Unpack_masked_sequence:string	CENSOR_masked_sequence
runCensor:jobid	CENSOR_job_ID
runCensor:jobid	EBI_CENSOR_poll_job:Job_ID
runCensor:jobid	Get_alignment:jobid
runCensor:jobid	Get_masked_sequence:jobid
runCensor:jobid	Get_table:jobid
Unpack_alignment:string	CENSOR_alignment
Unpack_table:string	CENSOR_table

Coordinations (3)

Controller	Target
EBI_CENSOR_poll_job	Get_masked_sequence
EBI_CENSOR_poll_job	Get_alignment
EBI_CENSOR_poll_job	Get_table

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

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Information Version 1 (earliest) (of 2)

Information Credits (1)

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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

2937 viewings

2342 downloads

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Citations (0)

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Version History

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EBI_CENSOR

Created by Hamish McWilliam on Tuesday 17 June 2008 20:42:46 (UTC)

Last edited by Hamish McWilliam on Tuesday 17 June 2008 20:42:47 (UTC)
EBI_CENSOR

Created by Hamish McWilliam on Tuesday 17 June 2008 20:42:46 (UTC)

Last edited by Hamish McWilliam on Wednesday 25 June 2008 06:16:03 (UTC)

Revision comment:

Complete meta-data for processors and correct a couple of typos.

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