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Biomart and Blast with concatinated gene id

Workflow Entry: Biomart and Blast with concatinated gene id

Created at: 13/12/10 @ 14:41:39 Last updated: 13/12/10 @ 14:47:55

Version 1 (of 1)

Version created on: 13/12/10 @ 14:41:39 by: Stian Soiland-Reyes | Revision comments Expand

Last edited on: 13/12/10 @ 14:47:55 by: Stian Soiland-Reyes

Title: Biomart and Blast with concatinated gene id

Type: Taverna 2

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Description

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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Workflow Components

Authors (1)

Titles (4)

Descriptions (2)

Inputs (0)

Processors (5)

Name	Type	Description
hsapiens_gene_ensembl	biomart
blast_ddbj	wsdl	See the Service entry for this web service.
program_value	stringconstant
database_value	stringconstant
Concatenate_gene_id	localworker

Beanshells (0)

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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Original Uploader

Stian Soiland-Reyes

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Information Attributions (2)

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Information Tags (9)

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Information Statistics

112 viewings

302 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - Biomart and Blast with concatinated gene id

Created on: Monday 13 December 2010 @ 14:41:39 (GMT)

Created by: Stian Soiland-Reyes

Last edited on: Monday 13 December 2010 @ 14:47:55 (GMT)

Last edited by: Stian Soiland-Reyes

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Other workflows that use similar services (50)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Original Uploader

Lebreton

retrieve protein sequence and do a high speed BLAST from DDBJ Web services (v1)

Created: 01/09/10 @ 17:16:24 | Last updated: 01/09/10 @ 17:18:45

Credits: Lebreton

Attributions: retrieve protein sequence and do a high speed BLAST and extract position from DDBJ Web services

License: Creative Commons Attribution-Share Alike 3.0 Unported License

retrieve protein sequence and do a high speed BLAST from DDBJ Web services informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : ddbjbct program : tblastn param : -b 100 -v 100

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 19 times | Downloaded: 13 times

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