Workflow Entry: EBI_Blast2InterPro

Created at: 07/06/08 @ 10:52:47 Last updated: 26/10/08 @ 20:45:46

Version 2 (latest) (of 2)

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

Title: EBI_Blast2InterPro

Type: Taverna 1

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Description

Perform a BLAST search add information about the InterPro matches associated with the hits.

This implementation uses:

1. EBI’s WSWUBlast web service (http://www.ebi.ac.uk/Tools/webservices/services/wublast) to perform the initial BLAST search against UniProtKB.

2. 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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Run

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Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/230/download?version=2
[ More Info Expand ]

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.

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)

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