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fetch_fasta

Workflow Entry: fetch_fasta

Created at: 20/03/09 @ 11:22:45 Last updated: 20/03/09 @ 11:29:16

Version 1 (of 1)

Version created on: 20/03/09 @ 11:22:45 by: Jumblejumble | Revision comments Expand

Last edited on: 20/03/09 @ 11:29:17 by: Jumblejumble

Title: fetch_fasta

Type: Taverna 1

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Description

This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain.

Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree.

The output is presented in a pdf format detailing this strain. Details include: putative identification, presence of MecA and phylogenic tree and ID of it and its neighbour strains.

This workflow is useful as it can easily be adapted to other projects with only minor modification to its processes.

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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:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/732/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (3)

Name	Description
sequenceIds
query_strain_id
email

Processors (18)

Name	Type	Description
Get_Nucleotide_FASTA	local
Write_Text_File	local
run_blastall	local
Read_FASTA	local
splitIDs	local
local_create_blastdb	local
ClustalW	local
Merge_FASTA	local
create_blastall_cmd_args	beanshell
create_formatdb_cmdArgs	beanshell	This beanshell will not be run until after the fasta file is written from the Write_Fasta_File processor. This beanshell creates an array of strings (a list of plain text), with each element containing one element of the arguments for the formatdb command line. Note that you can change the text in the beanshell in the element in the line after the one containing "-n" to set the name of the blast database you want. If you want to add any other command line arguments, follow the system in the beanshell. E.g. add the flag, e.g. "-x" in one line, and its argument "somethingOrOther" in another line.
parametersXML2	local
Neighbours	local
getNeighbours	arbitrarywsdl
addSequenceToFasta	arbitrarywsdl
getSequences	arbitrarywsdl
isMRSA	workflow
EBI_TCoffee	workflow
draw_tree	local

Beanshells (2)

Name	Description	Inputs	Outputs
create_blastall_cmd_args			cmdArgsList
create_formatdb_cmdArgs	This beanshell will not be run until after the fasta file is written from the Write_Fasta_File processor. This beanshell creates an array of strings (a list of plain text), with each element containing one element of the arguments for the formatdb command line. Note that you can change the text in the beanshell in the element in the line after the one containing "-n" to set the name of the blast database you want. If you want to add any other command line arguments, follow the system in the beanshell. E.g. add the flag, e.g. "-x" in one line, and its argument "somethingOrOther" in another line.		cmdArgsList

Outputs (5)

Name	Description
nuc_fasta
alignment
isMRSA
Neighbours
tree

Links (16)

Source	Sink
Get_Nucleotide_FASTA:outputText	Merge_FASTA:stringlist
Merge_FASTA:concatenated	Write_Text_File:filecontents
create_blastall_cmd_args:cmdArgsList	run_blastall:args
create_formatdb_cmdArgs:cmdArgsList	local_create_blastdb:args
sequenceIds	splitIDs:string
parametersXML2:output	getSequences:parameters
query_strain_id	isMRSA:sequenceId
Read_FASTA:filecontents	EBI_TCoffee:Sequences
email	EBI_TCoffee:Email_address
getNeighbours:parameters	Neighbours:input
splitIDs:split	Get_Nucleotide_FASTA:id
ClustalW:result	tree
EBI_TCoffee:TCoffee_alignment	alignment
Merge_FASTA:concatenated	nuc_fasta
Neighbours:return	Neighbours
isMRSA:isMRSA	isMRSA

Coordinations (9)

Controller	Target
Write_Text_File	create_formatdb_cmdArgs
local_create_blastdb	run_blastall
run_blastall	parametersXML2
getSequences	Read_FASTA
addSequenceToFasta	Read_FASTA
run_blastall	addSequenceToFasta
run_blastall	getNeighbours
Read_FASTA	ClustalW
ClustalW	draw_tree

Information Workflow Type

Taverna 1

Information Original Uploader

Jumblej...

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Jumblejumble

Information Attributions (0)

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None

Information Tags (11)

Original Uploader tags

alignment
|
beanshell
|
blastall
|
database
|
FASTA
|
fetch
|
file
|
list
|
strings
|
text
|
tree

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Information Statistics

497 viewings

601 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - fetch_fasta

Created on: Friday 20 March 2009 @ 11:22:45 (GMT)

Created by: Jumblejumble

Last edited on: Friday 20 March 2009 @ 11:29:17 (GMT)

Last edited by: Jumblejumble

Revision comments:

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This Workflow only has one version.

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Comments (1)

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Paul Fisher

Hi,

I think you may have some nested workflows in there that have not been uploaded (red boxes). Could you please check it and save it, choosing to embed the nested workflows?

cheers,

Paul