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Tag: BLAST User: Wassinki Licence: by-sa
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Workflow Mapping OligoNucleotides to an assembly (7)

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Version info The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes. ...

Created: 2009-02-13 | Last updated: 2009-02-13

Credits: User Wassinki User Pieter Neerincx

Attributions: Workflow Blat against ENSEMBLE Danio_rerio_Genome Workflow BlatBlastCombi Workflow Blast against ENSEMBLE Danio_rerio_Genome Workflow AppendToFile Blob Test Input for Mapping oligonucleotides to an assembly Blob Input for Mapping oligonucleotides to an assembly

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Workflow BlatBlastCombi (2)

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: User Wassinki

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Workflow Blast against ENSEMBLE Danio_rerio_Genome (1)

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: User Wassinki

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