Protein_alignment_transmembrane

Created: 2008-06-01 12:20:29

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Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges:

Sequence similarity search (SSS) to find homologues
Fetch sequences of hits
Multiple sequence alignment (MSA) of hit sequences
EMBOSS tmap with alignment from 3.

Uses the EBI web services:

WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta)
WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch)
WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2)
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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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.

Beanshells (2)

Name	Description	Inputs	Outputs
Is_Done		job_status	is_done
Is_done	Map job status into true/false is done flag	job_status	is_done

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)

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

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Taverna 1

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Hamish McWilliam

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Hamish McWilliam

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Information Statistics

3596 viewings

2833 downloads

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Protein_alignment_transmembrane

Created by Hamish McWilliam on Sunday 01 June 2008 12:20:29 (UTC)

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