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EBI_Blast2InterPro

Workflow Entry: EBI_Blast2InterPro

Created at: 26/10/08 @ 20:45:45 Last updated: 22/08/12 @ 11:22:43

Version 2 (latest) (of 2)

Version created on: 26/10/08 @ 20:45:45 by: Hamish McWilliam | Revision comment Expand

Last edited on: 01/04/11 @ 08:55:49 by: Hamish McWilliam

Title: EBI_Blast2InterPro

Type: Taverna 1

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Description

Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap) web services. Thus the workflow described here no longer works, see the alternative workflows for the InterProScan (SOAP) service for workflows which use the new services.

Perform a BLAST search add information about the InterPro matches associated with the hits. This implementation uses:

EBI’s WSWUBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/wublast) to perform the initial BLAST search against UniProtKB.
EBI’s WSDbfetch web service (http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) to retreive the sequences of the hits found by BLAST.

3. EBI’s WSInterProScan web service (http://www.ebi.ac.uk/Tools/webservices/services/interproscan) to get the InterPro matches for the BLAST hits.

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http://www.myexperiment.org/workflows/230/download?version=2
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Workflow Components

Inputs (2)

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

Processors (4)

Name	Type	Description
EBI_dbfetch_fetchBatch	workflow	Get the sequences for the hits found by WU-BLAST.
Fasta_string_to_fasta_list	workflow	Split the string containing the hit sequences into individual sequences.
EBI_InterProScan	workflow	Run InterProScan on the hits found by WU-BLAST.
EBI_WUBLAST	workflow	Find similar sequences using WU-BLAST.

Beanshells (4)

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_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		job_status	is_done

Outputs (8)

Name	Description
WUBLAST_job_ID	EBI identifer for the WU-BLAST job.
WUBLAST_result_text	WU-BLAST result in plain text format.
WUBLAST_hit_list	List of the identifiers of the hits found by WU-BLAST.
WUBLAST_hit_sequences	The sequences, in fasta format, of the hits found by WU-BLAST.
InterProScan_job_ID	EBI job identifer for the InterProScan jobs.
InterProScan_result_text	InterProScan results in plain text (tab-delimited) format.
InterProScan_result_XML	InterProScan results in XML format.
InterProScan_result_GFF

Links (14)

Source	Sink
Email_address	EBI_InterProScan:Email_address
Email_address	EBI_WUBLAST:E-mail Address
Sequence_or_ID	EBI_WUBLAST:Sequence or ID
EBI_InterProScan:InterProScan_GFF	InterProScan_result_GFF
EBI_WUBLAST:Hit ID list	EBI_dbfetch_fetchBatch:ID_list
EBI_InterProScan:InterProScan_XML_result	InterProScan_result_XML
EBI_InterProScan:InterProScan_text_result	InterProScan_result_text
EBI_InterProScan:Job_ID	InterProScan_job_ID
EBI_WUBLAST:Hit ID list	WUBLAST_hit_list
EBI_WUBLAST:Job_ID	WUBLAST_job_ID
EBI_WUBLAST:Text Result	WUBLAST_result_text
EBI_dbfetch_fetchBatch:Sequences	Fasta_string_to_fasta_list:fasta_string
Fasta_string_to_fasta_list:fasta_list	EBI_InterProScan:Sequence_or_ID
Fasta_string_to_fasta_list:fasta_list	WUBLAST_hit_sequences

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

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Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (4)

(Workflows/Files)

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Information Attributed By (1)

(Workflows/Files)

Multi sequences NCBI BLAST

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Information Statistics

2981 viewings

1703 downloads

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Citations (0)

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Version History

In chronological order:

EBI_Blast2InterPro

Created by Hamish McWilliam on Saturday 07 June 2008 @ 10:52:46 (UTC)
EBI_Blast2InterPro

Created by Hamish McWilliam on Sunday 26 October 2008 @ 20:45:45 (UTC)

Last edited by Hamish McWilliam on Friday 01 April 2011 @ 08:55:49 (UTC)

Revision comment:

Update for changes to the operation output names in the InterProScan web service. Also add an output for the GFF formated InterProScan results.

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Other workflows that use similar services (37)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Original Uploader

Hamish McWilliam

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Download (v2)

Protein_search_fetch_align_tree (2)

Created: 07/04/09 @ 20:13:19

Credits: Hamish McWilliam

Attributions: EBI_ClustalW2 EBI_ClustalW2_phylogentic_tree EBI_dbfetch_fetchBatch EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

An implmentation of the classical sequence analysis workflow: Find homologues (sequence similarity search) Fetch homologues Align homologues (multiple sequence alignment) Produce phylogenetic tree In this implementation the EBI webservices are used: WU-BLAST (WSWUBlast) blastp vs. UniProtKB dbfetch (WSDbfetch) ClustalW (WSClustalW2) ClustalW (WSClustalW2) Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers...