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Identify_strain_and_phylogenetic_tree

Workflow Entry: Identify_strain_and_phylogenetic_tree

Created at: 20/03/09 @ 15:20:36 Last updated: 20/03/09 @ 15:22:25

Version 1 (of 1)

Version created on: 20/03/09 @ 15:20:36 by: Aailyso | Revision comments Expand

Last edited on: 20/03/09 @ 15:22:26 by: Aailyso

Title: Identify_strain_and_phylogenetic_tree

Type: Taverna 1

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Workflow Components

Inputs (3)

Name	Description
ProteinID	Using housekeep gene code protein as parameter to build the phylip tree.
StrainXID
StrainX_url

Processors (10)

Name	Type	Description
Tree_View	local	this is the comand processor to invoke the treeview software and display the phylip tree which generated by clustalw
Write_Text_File	local
mecASearch	arbitrarywsdl	This processor is the local java code to parse the mecA gene from the EMBL file.
strainRecognizer	arbitrarywsdl	this is a local processor that recongnize the best hit of the blast result.
Get_Protein_FASTA	workflow	This retreive the protein sequence and generate as FASTA file
run_Clustalw	workflow	This work flow is a simple comand of clustalw. To make it run , you need to install clastalw to you local machine.
Get_Embl_File	workflow	retrieve the emble file based on the strainX url
Fetch_Seq	workflow	This nested workflow is from my experiment. using fetchBatch to retreive a list of sequence
Blast_localDB	workflow	This workflow is using local blast and local database to get the blast result of query sequence
WUBlast_Protein	workflow	This Nested workflow is come from my experiment. thanks the author here. Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params.

Beanshells (1)

Name	Description	Inputs	Outputs
Is_Done		job_status	is_done

Outputs (5)

Name	Description
Hit_Seq
Clustalw_Result
treeview
Hit_Strain_Id
Is_MRSA

Links (13)

Source	Sink
ProteinID	Get_Protein_FASTA:ProteinID
Blast_localDB:Blast_Result	strainRecognizer:parameters
Fetch_Seq:Sequences	Write_Text_File:filecontents
Get_Protein_FASTA:Protein_Seq	WUBlast_Protein:Sequence
StrainXID	Blast_localDB:Embl_id
StrainX_url	Get_Embl_File:embl_url
Get_Embl_File:Embl_File	mecASearch:parameters
Tree_View:result	treeview
WUBlast_Protein:Hit ID list	Fetch_Seq:ID_list
Write_Text_File:outputFile	Hit_Seq
mecASearch:parameters	Is_MRSA
run_Clustalw:output	Clustalw_Result
strainRecognizer:parameters	Hit_Strain_Id

Coordinations (2)

Controller	Target
Write_Text_File	run_Clustalw
run_Clustalw	Tree_View

Information Workflow Type

Taverna 1

Information Original Uploader

Aailyso

Information License

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Information Statistics

541 viewings

670 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Identify_strain_and_phylogenetic_tree

Created on: Friday 20 March 2009 @ 15:20:36 (GMT)

Created by: Aailyso

Last edited on: Friday 20 March 2009 @ 15:22:26 (GMT)

Last edited by: Aailyso

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Taverna 1

Original Uploader

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Created: 04/07/09 @ 11:39:54 | Last updated: 06/12/10 @ 10:56:44

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Attributions: EBI_WU-BLAST

License: Creative Commons Attribution 3.0 Unported License

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Taverna 1

Original Uploader

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

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License: Creative Commons Attribution 3.0 Unported License

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...

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Tags (15):