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Items tagged with "biomart" (14)

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Workflows (13)

Taverna 1 Original Uploader Alan Williams	BiomartAndEMBOSSAnalysis (v4) Created: 15/09/09 @ 15:11:11 License: Creative Commons Attribution 3.0 Unported License 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: 1075 times \| Downloaded: 373 times Tags (6): bioinformatics \| biomart \| emboss \| example \| mygrid \| taverna	View Download (v4)
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 Kieren Lythgow	Biomart Protein Sequence Retrieval (v1) Created: 09/03/09 @ 11:38:10 Credits: Kieren Lythgow License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 174 times \| Downloaded: 44 times Tags (5): biomart \| ensembl \| FASTA \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BioMart and Emboss Analysis (T2) (v1) Created: 15/09/09 @ 15:05:11 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 274 times \| Downloaded: 78 times Tags (5): alignment \| biomart \| clustalw \| emboss \| homology	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast (v1) Created: 13/12/10 @ 14:41:12 \| Last updated: 13/12/10 @ 15:15:45 Attributions: BLAST using DDBJ service License: Creative Commons Attribution 3.0 Unported License 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: 8 times \| Downloaded: 7 times Tags (15): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Biomart and Blast with concatinated gene id (v1) Created: 13/12/10 @ 14:41:39 \| Last updated: 13/12/10 @ 14:47:55 Attributions: BLAST using DDBJ service Biomart and Blast License: Creative Commons Attribution 3.0 Unported License 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: 12 times \| Downloaded: 8 times Tags (9): alignment \| biomart \| BLAST \| ddbj \| emboss \| human \| human sapiens \| rodent \| sequence alignment	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	BiomartAndEMBOSSAnalysis (v4) Created: 27/01/11 @ 17:03:03 \| Last updated: 12/05/11 @ 13:31:41 Credits: Katy Wolstencroft Alan Williams Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 97 times \| Downloaded: 55 times Tags (16): alignment \| biomart \| biomart emboss \| bonn \| disease \| emboss \| emma \| ensembl \| gene \| genes \| homolog \| human \| mouse \| sequence \| sequence alignment \| soaplab	View Download (v4)
Taverna 2 Original Uploader Rafael C. Jimenez	Find PRIDE experiments by GO (v1) Created: 29/05/11 @ 19:07:59 \| Last updated: 29/05/11 @ 19:08:01 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 5 times \| Downloaded: 6 times Tags (4): biomart \| ebi \| pride \| protein identifications	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find Reactome pathways and reactions by GO (v1) Created: 29/05/11 @ 19:09:23 \| Last updated: 29/05/11 @ 19:09:25 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 11 times \| Downloaded: 6 times Tags (5): biomart \| ebi \| pathway \| reaction \| reactome	View Download (v1)
BioExtract Server Original Uploader Yosr Bouhlal	Biomart SNP (v1) Created: 20/06/11 @ 20:55:23 \| Last updated: 05/07/11 @ 18:21:04 Credits: Yosr Bouhlal License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 21 times \| Downloaded: 2 times Tags (5): biomart \| human genome \| primers \| restriction enzyme \| snp	View Download (v1)
Taverna 2 Original Uploader Alan Williams	BiomartAndEMBOSSDisease (v1) Created: 12/07/11 @ 12:54:05 \| Last updated: 12/07/11 @ 12:54:07 Credits: Katy Wolstencroft Attributions: BiomartAndEMBOSSAnalysis License: Creative Commons Attribution 3.0 Unported License 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: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 6 times \| Downloaded: 4 times Tags (4): biomart \| emboss \| example \| taverna	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Biomart datasets for the Ensembl Genes mart service (v1) Created: 03/10/11 @ 10:17:40 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 2 times \| Downloaded: 2 times Tags (3): biomart \| datasets \| ensembl	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Find Orthologs for proteins in Ensembl (v1) Created: 03/10/11 @ 14:33:04 \| Last updated: 03/10/11 @ 14:33:07 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Find Orthologs for proteins in Ensembl using biomart. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 5 times Tags (4): biomart \| ensembl \| orthologous \| protein	View Download (v1)