About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
EBI_Blast2InterPro

Workflow Entry: EBI_Blast2InterPro

Created at: 26/10/08 @ 20:45:45 Last updated: 01/04/11 @ 08:55:49

Version 2 (latest) (of 2)

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

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

Title: EBI_Blast2InterPro

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

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Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

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.

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

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (4)

(Workflows/Files)

Information Tags (11)

Original Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Private pack

Log in to add to one of your Packs

Information Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (1)

(Workflows/Files)

Multi sequences NCBI BLAST

Information Favourited By (0)

No one

Information Statistics

2717 viewings

1422 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - EBI_Blast2InterPro

Created on: Saturday 07 June 2008 @ 10:52:46 (GMT)

Created by: Hamish McWilliam

Revision comments:

None

Latest Version:
[2] - EBI_Blast2InterPro

Created on: Sunday 26 October 2008 @ 20:45:45 (GMT)

Created by: Hamish McWilliam

Last edited on: Friday 01 April 2011 @ 08:55:49 (GMT)

Last edited by: Hamish McWilliam

Revision comments:

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

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

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

Protein_search_fetch_align_tree (v2)

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...

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 403 times | Downloaded: 133 times

Tags (15):