BiomartAndEMBOSSAnalysis
Created: 2014-01-14 15:26:22
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
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 |
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