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Protein_search_fetch_align_tree

Workflow Entry: Protein_search_fetch_align_tree

Created at: 07/04/09 @ 20:13:19

Version 2 (latest) (of 2)

Version created on: 07/04/09 @ 20:13:19 by: Hamish McWilliam | Revision comments Expand

Title: Protein_search_fetch_align_tree

Type: Taverna 1

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Description

An implmentation of the classical sequence analysis workflow:

Find homologues (sequence similarity search)
Fetch homologues
Align homologues (multiple sequence alignment)
Produce phylogenetic tree

In this implementation the EBI webservices are used:

WU-BLAST (WSWUBlast) blastp vs. UniProtKB
dbfetch (WSDbfetch)
ClustalW (WSClustalW2)
ClustalW (WSClustalW2)

Note: this version does not add the inital query sequence to the alignment, and so is most useful when used with the identifers of existing database entries.

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Option 1:

Launch in Taverna

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:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/210/download?version=2
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
Email	User e-mail address.
Sequence_or_ID	Input protein sequence. Either the actual sequence (fasta format recommended) or a sequence entry identifer in database:identifier format (e.g. uniprot:wap_rat).

Processors (6)

Name	Type	Description
SSS_program	stringconstant
Search_database	stringconstant
Fetch_sequences	workflow	Fecth the set of hit sequences using EBI's WSDbfetch service.
Phylogenetic_tree	workflow	Phylogentic tree from multiple sequence alignment using EBI's WSClustalW2 service.
SSS	workflow	Sequence similarity search (SSS) using EBI's WSWUBlast service.
MSA	workflow	Multiple sequence alignment (MSA) of the hit sequences using EBI's WSClustalW2 service.

Beanshells (3)

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

Outputs (9)

Name	Description
SSS_text	Sequence similarity search (SSS) text output.
SSS_XML	Sequence similarity search (SSS) XML output.
SSS_Hit_IDs	List of hit identifers from sequence similarity search (SSS).
SSS_job_id	Job identifier for sequence similarity search (SSS).
Hit_sequences	Sequences in fasta format found by sequence similarity search (SSS).
MSA_alignment	Multiple sequence alignment (MSA) output sequence alignment.
MSA_job_id	Job identifier for multiple sequence alignment (MSA).
Phylogenetic_tree_text	Phylogenetic tree in PHYLIP format for use with drawing programs.
Phylogenetic_tree_job_id	Job identifier for phylogenetic tree creation.

Links (19)

Source	Sink
Email	MSA:Email_address
Email	Phylogenetic_tree:Email_address
Email	SSS:E-mail Address
Sequence_or_ID	SSS:Sequence or ID
SSS:Hit ID list	Fetch_sequences:ID_list
SSS_program:value	SSS:BLAST Program
Search_database:value	Fetch_sequences:Database
Fetch_sequences:Sequences	Hit_sequences
Fetch_sequences:Sequences	MSA:Sequences
MSA:ClustalW_alignment	MSA_alignment
MSA:ClustalW_alignment	Phylogenetic_tree:Sequence_alignment
MSA:Job_ID	MSA_job_id
Phylogenetic_tree:ClustalW_phylip_tree	Phylogenetic_tree_text
Phylogenetic_tree:Job_ID	Phylogenetic_tree_job_id
SSS:Hit ID list	SSS_Hit_IDs
SSS:Job_ID	SSS_job_id
SSS:Text Result	SSS_text
SSS:XML Result	SSS_XML
Search_database:value	SSS:Search Database

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (4)

(Workflows/Files)

Information Tags (15)

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Information Featured In Packs (1)

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Information Attributed By (1)

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Private item

Information Favourited By (2)

Information Statistics

2567 viewings

1606 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Protein_search_fetch_align_tree

Created on: Saturday 31 May 2008 @ 21:09:15 (GMT)

Created by: Hamish McWilliam

Revision comments:

None

Latest Version:
[2] - Protein_search_fetch_align_tree

Created on: Tuesday 07 April 2009 @ 20:13:19 (GMT)

Created by: Hamish McWilliam

Revision comments:

Update for changes in WSClustalW2 web service nomenclature.

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Taverna 1

Original Uploader

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Viewed: 246 times | Downloaded: 94 times

Tags (11):