Nucleotide_InterProScan

Created: 2008-10-26 21:10:09 Last updated: 2011-04-01 08:54:21

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Run InterProScan using a nucleotide sequence as input.

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Workflow Components

Inputs (2)

Name	Description
Sequence_or_ID	Input nucleotide sequence. Either the actual sequence (fasta format) or an entry identifier in database:identifer format (e.g. embl:x01153).
Email_address	User e-mail address.

Processors (3)

Name	Type	Description
Nucleotide_ORF_translation	workflow	From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).
EBI_NCBI_BLAST	workflow
EBI_InterProScan	workflow

Beanshells (7)

Name	Description	Inputs	Outputs
Add_angle	For sequences where the angle bracket (>), denoting the start of the fasta formated sequence, was removed during the split, prepend it.	stripped_fasta	full_fasta
Is_sequence	Return true if the input is a sequence or false if the input is a sequence identifer (e.g. uniprot:wap_rat).	sequence	is_sequence
Is_done	Convert job status to true/false.	job_status	is_done
Found_hits		hit_list_str	found_hits
Coordinate		input	output
Is_done	Map status codes into true/false is done flag.	job_status	is_done
Format_as_GFF	Using the text output of InterProScan generate GFF format (see http://www.sanger.ac.uk/Software/formats/GFF/) output.	interproscan_text	interproscan_gff

Outputs (6)

Name	Description
InterProScan_result_text	InterProScan result in tab-delimited format.
InterProScan_result_XML	InterProScan result in XML format.
Translated_ORF_list
InterProScan_job_ID
NCBI_BLAST_job_ID
NCBI_BLAST_result_text

Links (11)

Source	Sink
Email_address	EBI_InterProScan:Email_address
Email_address	EBI_NCBI_BLAST:Email_address
Sequence_or_ID	Nucleotide_ORF_translation:Sequence_or_ID
EBI_InterProScan:InterProScan_XML_result	InterProScan_result_XML
EBI_InterProScan:InterProScan_text_result	InterProScan_result_text
EBI_InterProScan:Job_ID	InterProScan_job_ID
EBI_NCBI_BLAST:Sequence	EBI_InterProScan:Sequence_or_ID
EBI_NCBI_BLAST:Job_ID	NCBI_BLAST_job_ID
EBI_NCBI_BLAST:Text_result	NCBI_BLAST_result_text
Nucleotide_ORF_translation:Translated_ORF_list	EBI_NCBI_BLAST:Sequence_or_ID
Nucleotide_ORF_translation:Translated_ORF_list	Translated_ORF_list

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Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

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Information Version 2 (of 4)

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Hamish McWilliam

Information Attributions (5)

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Information Attributed By (1)

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Nucleotide InterProScan for the BioExtract Server

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Information Statistics

8462 viewings

3724 downloads

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In chronological order:

Nucleotide_InterProScan

Created by Hamish McWilliam on Friday 06 June 2008 21:45:09 (UTC)

Last edited by Hamish McWilliam on Friday 06 June 2008 21:45:10 (UTC)
Nucleotide_InterProScan

Created by Hamish McWilliam on Friday 06 June 2008 21:45:09 (UTC)

Last edited by Hamish McWilliam on Friday 06 June 2008 21:47:13 (UTC)

Revision comment:

With the nested workflows...
Nucleotide_InterProScan

Created by Hamish McWilliam on Friday 06 June 2008 21:45:09 (UTC)

Last edited by Hamish McWilliam on Saturday 07 June 2008 09:06:50 (UTC)

Revision comment:

Tweak BLAST filtering rules. Add additional metadata descriptions.
Nucleotide_InterProScan

Created by Hamish McWilliam on Sunday 26 October 2008 21:10:09 (UTC)

Last edited by Hamish McWilliam on Friday 01 April 2011 08:54:21 (UTC)

Revision comment:

Update for changes to poll output names in the WSInterProScan service. Also add GFF output from InterProScan.

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