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Items tagged with "blat" (6)

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Workflows (5)

Taverna 1 Original Uploader Wassinki	BlatBlastCombi (v2) Created: 03/02/09 @ 08:20:43 \| Last updated: 03/02/09 @ 08:28:06 Credits: Wassinki License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 ... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 107 times \| Downloaded: 52 times Tags (3): BLAST \| blat	View Download (v2)
Taverna 1 Original Uploader Wassinki	Blat against ENSEMBLE Danio_rerio_Genome (v1) Created: 15/10/08 @ 09:25:43 \| Last updated: 15/10/08 @ 09:27:23 Credits: Wassinki License: Creative Commons Attribution-Share Alike 3.0 Unported License The blat workflow invokes the blat services provided at www.bioinformatics.nl (author Pieter Neerincx). As input, it takes a database name (for example, Danio_rerio_Genome for Zebra Fish) and one or more sequences in Fasta format. The output will be a tab separated output of the blat. An eValue string constant is added to filter on the e-Value. Note, the e-Value is not exactly the same as the blast e-Value. To run this workflow, a certificate to access www.bioinformatics.nl needs to instal... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 100 times \| Downloaded: 33 times Tags (1): blat	View Download (v1)
Taverna 1 Original Uploader Wassinki	Mapping OligoNucleotides to an assembly (v7) Created: 13/02/09 @ 09:05:35 \| Last updated: 13/02/09 @ 09:08:20 Credits: Wassinki Pieter Neerincx Attributions: Blat against ENSEMBLE Danio_rerio_Genome BlatBlastCombi Blast against ENSEMBLE Danio_rerio_Genome AppendToFile Test Input for Mapping oligonucleotides to an assembly Input for Mapping oligonucleotides to an assembly License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. ... Rating: 0.0 / 5 (0 ratings) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 527 times \| Downloaded: 97 times Tags (7): biomart \| BLAST \| blat \| ensembl \| microarray \| r \| rshell	View Download (v7)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blat (v1) Created: 22/09/10 @ 13:18:55 \| Last updated: 22/09/10 @ 13:35:49 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 13 times Tags (9): alignment \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)
Taverna 1 Original Uploader Barbera van Schaik	Sff2Fasta_Blast_Blat_ParseBlast (v1) Created: 22/09/10 @ 13:22:57 \| Last updated: 22/09/10 @ 13:36:12 Credits: Barbera van Schaik Antoine van Kampen Angela Luijf Silvia Olabarriaga License: Creative Commons Attribution-Share Alike 3.0 Unported License Blast and Blat Roche 454 sequences against a reference database on the Dutch Life Science Grid Conversion of Roche 454 sequences to fasta Blat sequences against a database Blast sequences against a database Parse Blast results http://www.bioinformaticslaboratory.nl/ Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 15 times Tags (10): alignment \| BLAST \| blat \| conversion \| DNA \| grid \| moteur \| sequence \| taverna \| vbrowser	View Download (v1)