tmap_single_sequence

Created: 2008-06-01 14:27:12 Last updated: 2008-06-02 21:38:13

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Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

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Workflow Components

Inputs (1)

Name	Description
Sequence_or_ID	Input sequence to analyse for transmembrane regions. Either the actual sequence (fasta format recommended) or an entry identifer in database:identifer format (e.g. uniprot:LPHN2_RAT).

Processors (3)

Name	Type	Description
tmap	soaplabwsdl	Displays membrane spanning regions
Sequence_or_ID	workflow	For an entry identifer, fetch the sequence, otherwise ensure the sequence is in fasta format.
Format_as_GFF	beanshell

Beanshells (2)

Name	Description	Inputs	Outputs
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

Outputs (3)

Name	Description
tmap_report	Output of tmap describing the found transmembrane features.
tmap_plot	Plot showing the tmap score and the predicted transmembrane regions.
tmap_GFF

Links (6)

Source	Sink
Sequence_or_ID	Sequence_or_ID:Sequence_or_ID
Format_as_GFF:tmap_gff	tmap_GFF
Sequence_or_ID:Sequence	tmap:sequences_direct_data
tmap:outfile	Format_as_GFF:tmap_output
tmap:Graphics_in_PNG	tmap_plot
tmap:outfile	tmap_report

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Information Workflow Type

Taverna 1

Information Uploader

Hamish McWilliam

Information License

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Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (1)

(Workflows/Files)

Sequence_or_ID

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Information Attributed By (1)

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Protein_transmembrane_prediction

Information Favourited By (1)

Wotan

Information Statistics

3810 viewings

2602 downloads

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Citations (0)

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Version History

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tmap_single_sequence

Created by Hamish McWilliam on Sunday 01 June 2008 14:27:12 (UTC)

Last edited by Hamish McWilliam on Sunday 01 June 2008 14:27:13 (UTC)
tmap_single_sequence

Created by Hamish McWilliam on Sunday 01 June 2008 14:27:12 (UTC)

Last edited by Hamish McWilliam on Monday 02 June 2008 21:38:13 (UTC)

Revision comment:

Add GFF output.

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