Biomart Protein Sequence Retrieval

Created: 2009-03-09 11:38:10

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

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Workflow Components

Inputs (3)

Name	Description
Chromo
Start
End

Processors (1)

Name	Type	Description
hsapiens_gene_ensembl	biomart	Homo sapiens genes (NCBI36)

Beanshells (0)

Outputs (1)

Name	Description
Proteins

Links (4)

Source	Sink
Chromo	hsapiens_gene_ensembl:hsapiens_gene_ensembl.chromosome_name_filter
End	hsapiens_gene_ensembl:hsapiens_gene_ensembl.end_filter
Start	hsapiens_gene_ensembl:hsapiens_gene_ensembl.start_filter
hsapiens_gene_ensembl:hsapiens_gene_ensembl	Proteins