Biomart and Blast with concatinated gene id

Created: 2010-12-13 14:41:39 Last updated: 2010-12-13 14:47:55

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart).

Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report.

Referenced in the Taverna knowledge blog.

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Titles (4)

Descriptions (2)

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Processors (5)

Name	Type	Description
hsapiens_gene_ensembl	biomart
blast_ddbj	wsdl	Wsdl http://xml.nig.ac.jp/wsdl/Blast.wsdl Wsdl Operation searchSimple
program_value	stringconstant	Value blastn
database_value	stringconstant	Value ddbjrod
Concatenate_gene_id	localworker	Script output = string1 + "\n" + string2;

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Outputs (4)

Name	Description
gene_id
transcript_exon_intron
text_blast_out
concatinated

Datalinks (9)

Source	Sink
hsapiens_gene_ensembl:hsapiens_gene_ensembl.transcript_exon_intron	blast_ddbj:query
program_value:value	blast_ddbj:program
database_value:value	blast_ddbj:database
blast_ddbj:Result	Concatenate_gene_id:string2
hsapiens_gene_ensembl:hsapiens_gene_ensembl.ensembl_gene_id	Concatenate_gene_id:string1
hsapiens_gene_ensembl:hsapiens_gene_ensembl.ensembl_gene_id	gene_id
hsapiens_gene_ensembl:hsapiens_gene_ensembl.transcript_exon_intron	transcript_exon_intron
blast_ddbj:Result	text_blast_out
Concatenate_gene_id:output	concatinated

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Taverna 2

Information Uploader

Stian Soiland-Reyes

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Biomart and Blast with concatinated gene id

Created by Stian Soiland-Reyes on Monday 13 December 2010 14:41:39 (UTC)

Last edited by Stian Soiland-Reyes on Monday 13 December 2010 14:47:55 (UTC)

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Biomart and Blast with concatinated gene id

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