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.

The InterProScan tool (http://www.ebi.ac.uk/Tools/InterProScan/) searches a protein sequence against a selection of protein domain, feature and family signature databases, and integrates the results giving potential assignments to InterPro entries and Gene Ontology terms. Since InterProScan is a protein search tool to use it with a nucleotide sequence, the sequence must be translated into a protein sequence. There are a number of ways of doing this, depending on the properties of the nucleotide sequence, in this case a simple open reading frame (ORF) model is used to obtain the candidate translations. These translations are filtered for length (>80aa) and a search against UniProtKB (http://www.uniprot.org/) is performed to ensure that only sequences which have some relationship with known protein space, on which the signatures used are based, are passed to InterProScan. Once the set of translations has been filtered the remaining sequences as passed on to InterProScan for analysis.

Note: the coordinates in the InterProScan output are in protein coordinates relative to the input translated sequence, to map these on to the input nucleotide sequence see the fasta header of the corresponding translated ORF where the nucleotide coordinates are shown.

This implementation uses:

EBI's WSDbfetch web service (http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) to retreive enties specified by database identifer.
EMBOSS seqret tool (http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html) via Soaplab (http://www.ebi.ac.uk/Tools/webservices/soaplab/overview) to ensure input sequences are in an appropriate format (i.e. fasta format).
EMBOSS getorf tool (http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/getorf.html) via Soaplab (http://www.ebi.ac.uk/Tools/webservices/soaplab/overview) to find the ORFs, perform the translation and filter the translations for length.
EBI's WSNCBIBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast) to perform the filtering BLAST search against UniProtKB.
EBI's WSInterProScan web service (http://www.ebi.ac.uk/Tools/webservices/services/interproscan) to access InterProScan for the final search.

and is based on the proceedure described for nucleotide InterProScan searches described on the WSInterProScan web pages (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan).

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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
EBI_InterProScan	workflow	Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). InterProScan returns a set of InterPro and InterPro member matches with your sequence, along with GO term assignments.
EBI_NCBI_BLAST	workflow	Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. For use with InterProScan the expectation threshold (exp) has been set to 0.00001 and the maximum number of hits to report has been set to 10. The input sequences which find hits are returned via the "Sequences" output.
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).

Beanshells (7)

Name	Description	Inputs	Outputs
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
Is_done	Convert job status to true/false.	job_status	is_done
Found_hits	Return true if hits were found.	hit_list_str	found_hits
Coordinate	Simple passthough used to coordinate with "Found_hits".	input	output
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

Outputs (6)

Name	Description
InterProScan_result_text	InterProScan result in tab-delimited format.
InterProScan_result_XML	InterProScan result in XML format.
Translated_ORF_list	List of the translated open reading frame (ORF) sequences which are longer than 80aa, which were passed to the BLAST.
InterProScan_job_ID	EBI job identifer for the InterProScan job.
NCBI_BLAST_job_ID	EBI job identifer for the NCBI BLAST job.
NCBI_BLAST_result_text	The NCBI BLAST ouput for each of the translated open reading frame (ORF) input sequences.

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_NCBI_BLAST:Sequence	EBI_InterProScan:Sequence_or_ID
Nucleotide_ORF_translation:Translated_ORF_list	EBI_NCBI_BLAST: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:Job_ID	NCBI_BLAST_job_ID
EBI_NCBI_BLAST:Text_result	NCBI_BLAST_result_text
Nucleotide_ORF_translation:Translated_ORF_list	Translated_ORF_list

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Hamish McWilliam

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Nucleotide InterProScan for the BioExtract Server

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Version History

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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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