Workflow Entry: tmap_single_sequence

Created at: 01/06/08 @ 14:27:13 Last updated: 02/06/08 @ 21:38:13

Version 2 (latest) (of 2)

Version created on: 01/06/08 @ 14:27:12 by: Hamish McWilliam | Revision comments Expand

Last edited on: 02/06/08 @ 21:38:13 by: Hamish McWilliam

Title: tmap_single_sequence

Type: Taverna 1

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Description

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

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Option 1:

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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:

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http://www.myexperiment.org/workflows/215/download?version=2
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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

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)

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