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BiomartAndEMBOSSAnalysis

Workflow Entry: BiomartAndEMBOSSAnalysis

Created at: 15/09/09 @ 15:11:11

Version 4 (latest) (of 4)

Version created on: 15/09/09 @ 15:11:11 by: Katy Wolstencroft | Revision comments Expand

Title: BiomartAndEMBOSSAnalysis

Type: Taverna 1

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Description

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

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Option 1:

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Option 2:

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http://www.myexperiment.org/workflows/158/download?version=4
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Workflow Components

Inputs (0)

Processors (10)

Name	Type	Description
FlattenImageList	local
GetUniqueHomolog	beanshell
CreateFasta	beanshell
seqret	soaplabwsdl	Reads and writes (returns) sequences
plot	soaplabwsdl	Displays aligned sequences, with colouring and boxing
emma	soaplabwsdl	Multiple alignment program - interface to ClustalW program
hsapiensGeneEnsembl	biomart	Homo sapiens genes (GRCh37)
getMMusSequence	biomart	Mus musculus genes (NCBIM37)
getRNorSequence	biomart	Rattus norvegicus genes (RGSC3.4)
getHSapSequence	biomart	Homo sapiens genes (GRCh37)

Beanshells (2)

Name	Description	Inputs	Outputs
GetUniqueHomolog		HSGeneIDs MouseGeneIDs RatGeneIDs	HSOut RatOut MouseOut
CreateFasta		hsSeq mmSeq rnSeq	fasta

Outputs (4)

Name	Description
outputPlot	The array of png images returned from the plot processor
HSapIDs
MMusIDs
RNorIDs

Links (17)

Source	Sink
CreateFasta:fasta	seqret:sequence_direct_data
GetUniqueHomolog:HSOut	getHSapSequence:hsapiens_gene_ensembl.ensembl_gene_id_filter
GetUniqueHomolog:MouseOut	getMMusSequence:mmusculus_gene_ensembl.ensembl_gene_id_filter
GetUniqueHomolog:RatOut	getRNorSequence:rnorvegicus_gene_ensembl.ensembl_gene_id_filter
emma:outseq	plot:sequences_direct_data
getHSapSequence:hsapiens_gene_ensembl.coding_gene_flank	CreateFasta:hsSeq
getMMusSequence:mmusculus_gene_ensembl.coding_gene_flank	CreateFasta:mmSeq
getRNorSequence:rnorvegicus_gene_ensembl.coding_gene_flank	CreateFasta:rnSeq
hsapiensGeneEnsembl:hsapiens_gene_ensembl.ensembl_gene_id	GetUniqueHomolog:HSGeneIDs
hsapiensGeneEnsembl:hsapiens_gene_ensembl.mouse_ensembl_gene	GetUniqueHomolog:MouseGeneIDs
hsapiensGeneEnsembl:hsapiens_gene_ensembl.rat_ensembl_gene	GetUniqueHomolog:RatGeneIDs
plot:Graphics_in_PNG	FlattenImageList:inputlist
seqret:outseq	emma:sequence_direct_data
FlattenImageList:outputlist	outputPlot
GetUniqueHomolog:HSOut	HSapIDs
GetUniqueHomolog:MouseOut	MMusIDs
GetUniqueHomolog:RatOut	RNorIDs

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Alan Williams

Information License

All versions of this Workflow are licensed under:

Information Credits (0)

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None

Information Attributions (0)

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Information Tags (6)

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Information Shared with Groups (1)

Taverna 1.7.1 workflow workbench examples

Information Featured In Packs (1)

Taverna 1.7 starter pack

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Information Ratings (0)

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Information Attributed By (5)

(Workflows/Files)

Item doesn't exist anymore
BioMart and Emboss Analysis (T2)
Item doesn't exist anymore
Biomart and EMBOSS analysis
BiomartAndEMBOSSAnalysis

Information Favourited By (1)

AbuJarour

Information Statistics

4154 viewings

2776 downloads

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Citations (0)

None

Version History

Earliest Version:
[1] - BiomartAndEMBOSSAnalysis

Created on: Wednesday 05 March 2008 @ 14:01:16 (GMT)

Created by: Alan Williams

Last edited on: Tuesday 25 March 2008 @ 14:44:01 (GMT)

Last edited by: Alan Williams

Revision comments:

None

Previous Versions:
[2] - BiomartAndEMBOSSAnalysis

Created on: Wednesday 05 March 2008 @ 14:01:16 (GMT)

Created by: Alan Williams

Last edited on: Thursday 27 March 2008 @ 12:14:09 (GMT)

Last edited by: Alan Williams

Revision comments:

This version has a description

[3] - BiomartAndEMBOSSAnalysis

Created on: Wednesday 05 March 2008 @ 14:01:16 (GMT)

Created by: Alan Williams

Last edited on: Monday 01 September 2008 @ 13:57:23 (GMT)

Last edited by: Alan Williams

Revision comments:

BioMart functionality changed

Latest Version:
[4] - BiomartAndEMBOSSAnalysis

Created on: Tuesday 15 September 2009 @ 15:11:11 (GMT)

Created by: Katy Wolstencroft

Revision comments:

Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the number of alignments returned becuase it is an example workflow. This option is no longer available through BioMart, so this version returns all sequences on your chosen chromosome. To reduce the number of sequences returned during testing, try changing the filter on the hsapiens_gene_ensembl to the Y chromosome, or change the base pair range.