Workflow Entry: Protein_alignment_transmembrane

Created at: 01/06/08 @ 12:20:30 Last updated: 01/06/08 @ 12:20:31

Version 1 (of 1)

Version created on: 01/06/08 @ 12:20:29 by: Hamish McWilliam | Revision comments Expand

Title: Protein_alignment_transmembrane

Type: Taverna 1

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Description

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3.

Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2) 4. Soaplab EMBOSS tmap

Note: currently this workflow does not attempt to add the query sequence into the set of sequences passed to the multiple alignment. Thus it is most suitable for searches using entires which are persent in the searched database (i.e. will be included via the self hit).

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http://www.myexperiment.org/workflows/213/download?version=1
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Workflow Components

Inputs (2)

Name	Description
Email	User e-mail address.
Sequence_or_ID	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 (6)

Name	Type	Description
SSS	workflow	Find homologues for the input sequence via a sequence similarity search (SSS). In this case FASTA is used.
Fetch_hits	workflow	Get the sequences for the hits from the sequence similarity search (SSS) to be used for the multiple sequence alignment (MSA).
Database	stringconstant	Database to search in the sequence similarity search (SSS) step.
SSS_program	stringconstant	Program to use for the sequence similarity search (SSS).
MSA	workflow	Perform a multiple sequence alignment (MSA) using the sequences found by the sequence similarity search (SSS).
tmap	soaplabwsdl	From the multiple sequence alignment (MSA) predict the transmembrane regions.

Outputs (6)

Name	Description
SSS_job_ID	EBI job identifer for the sequence similarity search.
MSA_job_ID	EBI job identifer for the multiple sequence alignment (MSA).
tmap_prediction	Report from tmap describing the predicted transmembrane regions.
SSS_hit_IDs	Identifiers of the entries found by the sequence similarity search (SSS).
MSA_alignment	The multiple sequence alignment (MSA) produced for input to tmap.
tmap_plot	Plot of the score used by tmap and the predicted regions.

Links (15)

Sink	Source
MSA:Email_address	Email
SSS:E-mail	Email
SSS:Sequence_or_ID	Sequence_or_ID
Fetch_hits:Database	Database:value
SSS:Database	Database:value
MSA:Sequences	Fetch_hits:Sequences
MSA_alignment	MSA:ClustalW_alignment
tmap:sequences_direct_data	MSA:ClustalW_alignment
MSA_job_ID	MSA:Job_ID
Fetch_hits:ID_list	SSS:Hit_ID_List
SSS_hit_IDs	SSS:Hit_ID_List
SSS_job_ID	SSS:Job_ID
SSS:FASTA_Program	SSS_program:value
tmap_plot	tmap:Graphics_in_PNG
tmap_prediction	tmap:outfile