BiomartAndEMBOSSAnalysis

Created: 2009-09-15 15:11:11 Last updated: 2015-01-26 13:03:32

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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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Workflow Components

Inputs (0)

Processors (10)

Name	Type	Description
FlattenImageList	local
getHSsequence	biomart	Homo sapiens genes (NCBI36)
getMMsequence	biomart	Mus musculus genes (NCBIM36)
getRNsequence	biomart	Rattus norvegicus genes (RGSC3.4)
hsapiens_gene_ensembl	biomart	Homo sapiens genes (NCBI36)
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

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
FlattenImageList:outputlist	outputPlot
GetUniqueHomolog:HSOut	HSapIDs
GetUniqueHomolog:HSOut	getHSsequence:hsapiens_gene_ensembl.ensembl_gene_id_filter
GetUniqueHomolog:MouseOut	MMusIDs
GetUniqueHomolog:MouseOut	getMMsequence:mmusculus_gene_ensembl.ensembl_gene_id_filter
GetUniqueHomolog:RatOut	RNorIDs
GetUniqueHomolog:RatOut	getRNsequence:rnorvegicus_gene_ensembl.ensembl_gene_id_filter
emma:outseq	plot:sequences_direct_data
getHSsequence:hsapiens_gene_ensembl.coding_gene_flank	CreateFasta:hsSeq
getMMsequence:mmusculus_gene_ensembl.coding_gene_flank	CreateFasta:mmSeq
getRNsequence:rnorvegicus_gene_ensembl.coding_gene_flank	CreateFasta:rnSeq
hsapiens_gene_ensembl:hsapiens_gene_ensembl.ensembl_gene_id	GetUniqueHomolog:HSGeneIDs
hsapiens_gene_ensembl:hsapiens_gene_ensembl.mouse_ensembl_gene	GetUniqueHomolog:MouseGeneIDs
hsapiens_gene_ensembl:hsapiens_gene_ensembl.rat_ensembl_gene	GetUniqueHomolog:RatGeneIDs
plot:Graphics_in_PNG	FlattenImageList:inputlist
seqret:outseq	emma:sequence_direct_data

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Information Workflow Type

Taverna 1

Information Uploader

Alan Williams

Information License

All versions of this Workflow are licensed under:

Information Version 3 (of 4)

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Taverna 1.7.1 workflow workbench examples

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Information Attributed By (5)

(Workflows/Files)

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

Information Favourited By (3)

Information Statistics

12183 viewings

7875 downloads

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Version History

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BiomartAndEMBOSSAnalysis

Created by Alan Williams on Wednesday 05 March 2008 14:01:16 (UTC)

Last edited by Alan Williams on Tuesday 25 March 2008 14:44:01 (UTC)
BiomartAndEMBOSSAnalysis

Created by Alan Williams on Wednesday 05 March 2008 14:01:16 (UTC)

Last edited by Alan Williams on Thursday 27 March 2008 12:14:09 (UTC)

Revision comment:

This version has a description
BiomartAndEMBOSSAnalysis

Created by Alan Williams on Wednesday 05 March 2008 14:01:16 (UTC)

Last edited by Alan Williams on Monday 01 September 2008 13:57:23 (UTC)

Revision comment:

BioMart functionality changed
BiomartAndEMBOSSAnalysis

Created by Katy Wolstencroft on Tuesday 15 September 2009 15:11:11 (UTC)

Revision comment:

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.

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