Protein_search_fetch_align_tree

Created: 2009-04-07 20:13:19

Download Workflow

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/210/download?version=1
[ 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 Uploader

Hamish McWilliam

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 2)

Information Credits (1)

(People/Groups)

Hamish McWilliam

Information Attributions (4)

(Workflows/Files)

Information Tags (15)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (1)

Private pack

Log in to add to one of your Packs

Information Attributed By (2)

(Workflows/Files)

Blast_Align_and_Tree
Private item

Information Favourited By (2)

Information Statistics

5809 viewings

3654 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Protein_search_fetch_align_tree

Created by Hamish McWilliam on Saturday 31 May 2008 21:09:15 (UTC)
Protein_search_fetch_align_tree

Created by Hamish McWilliam on Tuesday 07 April 2009 20:13:19 (UTC)

Revision comment:

Update for changes in WSClustalW2 web service nomenclature.

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (26)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

Protein_alignment_transmembrane (1)

Download

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/servic...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

Taverna 2

Uploader

Achille Zappa

Workflow for Automated Comparative Protein... (2)

Download

This workflow performs "parallel" generic protein sequence analysis. In order to do that a list of known protein identifiers chosen by the biologist enters into the software to perform different multiple sequence alignments and finally phylogenetic analysis.

Created: 2010-06-29 | Last updated: 2010-08-31

Credits: Achille Zappa

Attributions: EBI_ClustalW_alignment_tree