Workflow Entry: Protein_search_fetch_align_tree

Created at: 31/05/08 @ 21:09:18

Version 1 (of 1)

Version created on: 31/05/08 @ 21:09:15 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: 1. Find homologues (sequence similarity search) 2. Fetch homologues 3. Align homologues (multiple sequence alignment) 4. Produce phylogenetic tree

In this implementation the EBI webservices are used: 1. WU-BLAST (WSWUBlast) blastp vs. UniProtKB 2. dbfetch (WSDbfetch) 3. ClustalW (WSClustalW2) 4. 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:

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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/210/download?version=1
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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.

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)

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