Identify_strain_and_phylogenetic_tree

Created: 2009-03-20 15:20:36 Last updated: 2009-03-20 15:22:25

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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

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Taverna 1

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Aailyso

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2420 viewings

2239 downloads

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Identify_strain_and_phylogenetic_tree

Created by Aailyso on Friday 20 March 2009 15:20:36 (UTC)

Last edited by Aailyso on Friday 20 March 2009 15:22:26 (UTC)

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EBI_WU-BLAST (1)

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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. Note: the WSWUBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement WU-BLAST services (REST or SOAP) should be used instead.

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam