Workflow Entry: BiomartAndEMBOSSAnalysis

Created at: 05/03/08 @ 14:01:18 Last updated: 01/09/08 @ 13:57:23

Version 3 (latest) (of 3)

Version created on: 05/03/08 @ 14:01:16 by: Alan Williams | Revision comments Expand

Last edited on: 01/09/08 @ 13:57:23 by: Alan Williams

Title: BiomartAndEMBOSSAnalysis

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

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.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

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/158/download?version=3
[ More Info Expand ]

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

Outputs (4)

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

Links (17)

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