myExperiment - Workflows - Protein_transmembrane_prediction (Hamish McWilliam) [Taverna 1 Workflow]

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).

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.

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

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.

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

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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?

Workflow Entry: Protein_transmembrane_prediction

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