Biomart and Blast

Created: 2010-12-13 14:41:12 Last updated: 2010-12-13 15:15:45

Download Workflow

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)

Referenced in the Taverna knowledge blog.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/1726/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (4)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (4)

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

Beanshells (0)

Outputs (3)

Name	Description
gene_id
transcript_exon_intron
text_blast_out

Datalinks (6)

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
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

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Stian Soiland-Reyes

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (0)

(People/Groups)

None

Information Attributions (1)

(Workflows/Files)

BLAST using DDBJ service

Information Tags (9)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

myGrid

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (1)

(Workflows/Files)

Biomart and Blast with concatinated gene id

Information Favourited By (1)

Vz33

Information Statistics

2507 viewings

1708 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Biomart and Blast

Created by Stian Soiland-Reyes on Monday 13 December 2010 14:41:12 (UTC)

Last edited by Stian Soiland-Reyes on Monday 13 December 2010 15:15:45 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

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

Uploader

Paul Fisher

BLASTP with simplified results returned (2)

Download

Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output. Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV...

Created: 2007-10-03 | Last updated: 2009-12-03