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Items tagged with "biomart" (14)

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Workflows (13)
Original Uploader

Workflow BiomartAndEMBOSSAnalysis (4)

Created: 15/09/09 @ 15:11:11

License: Creative Commons Attribution 3.0 Unported License

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 1256 times | Downloaded: 421 times

Tags (6):

Original Uploader

Workflow Mapping OligoNucleotides to an assembly (7)

Created: 13/02/09 @ 09:05:35 | Last updated: 13/02/09 @ 09:08:20

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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. ...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 627 times | Downloaded: 115 times

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Original Uploader

Workflow Biomart Protein Sequence Retrieval (1)

Created: 09/03/09 @ 11:38:10

Credits: User Kieren Lythgow

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow queries Biomart to retrieve the Ensembl gene id, protein id, gene name, description and amino acid sequence from the Ensembl Homo sapiens dataset. The user needs to specify a defined chromosomal region i.e. Chromo = 1, Start = 100000000, End = 250000000. This returns all unique entries in FASTA format.

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

Viewed: 200 times | Downloaded: 48 times

Tags (5):

Original Uploader

Workflow BioMart and Emboss Analysis (T2) (1)

Created: 15/09/09 @ 15:05:11

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

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

Viewed: 311 times | Downloaded: 91 times

Tags (5):

Original Uploader

Workflow Biomart and Blast (1)

Created: 13/12/10 @ 14:41:12 | Last updated: 13/12/10 @ 15:15:45

Attributions: Workflow BLAST using DDBJ service

License: Creative Commons Attribution 3.0 Unported License

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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) Referenced in the Taverna knowledge blog.

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

Viewed: 18 times | Downloaded: 12 times

Tags (15):

Original Uploader

Workflow Biomart and Blast with concatinated gene id (1)

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

Attributions: Workflow BLAST using DDBJ service Workflow Biomart and Blast

License: Creative Commons Attribution 3.0 Unported License

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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.

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

Viewed: 20 times | Downloaded: 14 times

Tags (9):

Original Uploader

Workflow BiomartAndEMBOSSDisease (4)

Created: 27/01/11 @ 17:03:03 | Last updated: 04/09/12 @ 09:32:08

Credits: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 131 times | Downloaded: 74 times

Tags (16):

Original Uploader

Workflow Find PRIDE experiments by GO (1)

Created: 29/05/11 @ 19:07:59 | Last updated: 29/05/11 @ 19:08:01

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

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

Viewed: 52 times | Downloaded: 8 times

Tags (4):

Original Uploader

Workflow Find Reactome pathways and reactions by GO (1)

Created: 29/05/11 @ 19:09:23 | Last updated: 29/05/11 @ 19:09:25

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

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

Viewed: 34 times | Downloaded: 8 times

Tags (5):

Original Uploader

Workflow Biomart SNP (1)

Created: 20/06/11 @ 20:55:23 | Last updated: 05/07/11 @ 18:21:04

Credits: User Yosr Bouhlal

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Normal 0 false false false EN-US X-NONE AR-SA /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyl...

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 30 times | Downloaded: 7 times

Tags (5):

Original Uploader

Workflow BiomartAndEMBOSSDisease (2)

Created: 12/07/11 @ 12:54:05 | Last updated: 19/03/12 @ 15:31:14

Credits: User Katy Wolstencroft

Attributions: Workflow BiomartAndEMBOSSDisease

License: Creative Commons Attribution 3.0 Unported License

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 21 times

Tags (4):

Original Uploader

Workflow Biomart datasets for the Ensembl Genes mar... (1)

Created: 03/10/11 @ 10:17:40

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Retrieve Biomart datasets for the Ensembl Genes mart service (one dataset per specie).

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

Viewed: 12 times | Downloaded: 10 times

Tags (3):

Original Uploader

Workflow Find Orthologs for proteins in Ensembl (1)

Created: 03/10/11 @ 14:33:04 | Last updated: 03/10/11 @ 14:33:07

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Orthologs for proteins in Ensembl using biomart.

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

Viewed: 15 times | Downloaded: 8 times

Tags (4):

Packs (1)
Creator

Pack Package: mapping oligonucleotides to an assembly


Created: 11/12/08 @ 12:02:47 | Last updated: 22/01/09 @ 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"  

0 items in this pack

Comments: 0 | Viewed: 176 times | Downloaded: 60 times

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