Protein_transmembrane_prediction

Created: 2008-10-26 21:16:10 Last updated: 2011-04-01 08:57:10

Download Workflow

Note: the WSInterProScan web service used by this workflow is no longer available haveing been replaced by the EMBL-EBI's InterProScan (REST) (http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_rest) and InterProScan (SOAP)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

Transmembrane and signal peptide prediction using three methods:

EMBOSS tmap with a single sequence. Uses Soaplab tmap.
Phobius. Uses EBI's WSPhobius web service.
TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service.

The results of the three methods are converted into GFF format and collated.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/216/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
Email	User e-mail address.
Sequence_or_ID	Sequence to analyse. Either the actual sequence (fasta format recommended) or an entry identifier in database:identifer format (e.g. uniprot:LPHN2_RAT).

Processors (4)

Name	Type	Description
EBI_Phobius	workflow	Predict transmembrane domains and signal peptide using Phobius.
EBI_InterProScan_tmhmm_signalp	workflow	Predict transmembrane regions using TMHMM and signal peptide using SignalP.
tmap_single_seq	workflow	Transmembrane region prediction using EMBOSS tmap.
Merge_GFF	beanshell	Collate GFF output from the prediction methods.

Beanshells (7)

Name	Description	Inputs	Outputs
Is_done		job_status	is_done
Format_as_GFF		phobius_output	phobius_gff
Is_done	Map status codes into true/false is done flag.	job_status	is_done
Format_as_GFF		interproscan_text_result	gff_result
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
Format_as_GFF		tmap_output	tmap_gff
Merge_GFF	Collate GFF output from the prediction methods.	gff_input1 gff_input2 gff_input3	gff_output

Outputs (4)

Name	Description
Phobius_output	Predictions from Phobius.
InterProScan_output	InterProScan methods TMHMM and SignalP predictions.
tmap_output	EMBOSS tmap prediction, from single sequence input.
GFF_output	Collated feature predictions in GFF format.

Links (12)

Source	Sink
Email	EBI_InterProScan_tmhmm_signalp:Email_address
Email	EBI_Phobius:Email
Sequence_or_ID	EBI_InterProScan_tmhmm_signalp:Sequence_or_ID
Sequence_or_ID	EBI_Phobius:Sequence_or_ID
Sequence_or_ID	tmap_single_seq:Sequence_or_ID
EBI_InterProScan_tmhmm_signalp:GFF_result	Merge_GFF:gff_input2
EBI_Phobius:Phobius_GFF	Merge_GFF:gff_input1
tmap_single_seq:tmap_GFF	Merge_GFF:gff_input3
EBI_InterProScan_tmhmm_signalp:InterProScan_text_result	InterProScan_output
EBI_Phobius:Phobius_output	Phobius_output
Merge_GFF:gff_output	GFF_output
tmap_single_seq:tmap_report	tmap_output

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (3)

(Workflows/Files)

Information Tags (11)

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 Attributed By (0)

(Workflows/Files)

None

Information Favourited By (2)

Information Statistics

5185 viewings

3170 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Protein_transmembrane_prediction

Created by Hamish McWilliam on Sunday 01 June 2008 17:49:30 (UTC)
Protein_transmembrane_prediction

Created by Hamish McWilliam on Sunday 26 October 2008 21:16:10 (UTC)

Last edited by Hamish McWilliam on Friday 01 April 2011 08:57:10 (UTC)

Revision comment:

Update for changes in the WSInterProScan web service.

Reviews (0)

No reviews yet

Be the first to review!

Comments (3)

View Timeline

Log in to make a comment

Niall Haslam

Any chance of getting the subworkflows for this as well. Couldn't find them online and I want the polling part. i.e. For loads of the EBI jobs, you have to write beanshells to check if the job is done. It would nice to see a write up on how to create workflows for this.

Thanks,

Niall

Hamish McWilliam

Hi Niall. The subworkflows are included. If you download this workflow, load it into Taverna and navigate to the nexted workflows you can save them indpendantly using the normal save functionality.

The general process required to poll for service results is explained on the EBI website (see http://www.ebi.ac.uk/Tools/webservices/tutorials/workflow/taverna). In brief it uses Taverna's retry mechanism and a nested workflow which fails if the job has not completed.

Giovanni Dall'Olio

Great!

With which proteins have you tried this workflow? Do you have an estimate for its precision/accuracy?

There are other protein structure preditors that merge results from various sources, and combine them, to obtain a better prediction.
Is this the same approach you are using in this protocol?
e.g. I know of this predictor (http://pongo.biocomp.unibo.it/), but it is only for membrane proteins structure. Is it something similar?

How are the gff results merged at the end of the workflow? What does Gff_output contains, exactly?