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Items tagged with "biomart" (5)

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Packs (1)

Creator:

Wassinki

Package: mapping oligonucleotides to an assembly

Created: 11/12/08 @ 12:02:48 | Last updated: 22/01/09 @ 09:06:27

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

5 items in this pack

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Workflows (4)

Taverna 1

Original Uploader

Alan Williams

BiomartAndEMBOSSAnalysis (v4)

Created: 05/03/08 @ 14:01:18 | Last updated: 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: 552 times | Downloaded: 219 times

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Taverna 1

Original Uploader

Wassinki

Mapping OligoNucleotides to an assembly (v7)

Created: 11/12/08 @ 12:11:59 | Last updated: 13/02/09 @ 09:08:23

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: 207 times | Downloaded: 41 times

Tags (7):

biomart
|
BLAST
|
blat
|
ensembl
|
microarray
|
r
|
rshell

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Taverna 1

Original Uploader

Kieren Lythgow

Biomart Protein Sequence Retrieval (v1)

Created: 09/03/09 @ 11:38:10 | Last updated: 09/03/09 @ 11:38:11

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

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Taverna 2

Original Uploader

Katy Wolstencroft

BioMart and Emboss Analysis (T2) (v1)

Created: 15/09/09 @ 15:05:12

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: 134 times | Downloaded: 30 times

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