Question: Retrieve Genomic Ranges From Ensembl Genomes Using Gene Names
1
gravatar for Anima Mundi
6.9 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

Hello, I would like to extract the genomic coordinates from a series of genes using a common substring of their gene names. For example, the method should output, for the name "tubulin", the ranges (i.e. in BED format) of all the genes in the genome (i.e. mouse) containing "tubulin" (i.e. alpha, beta, gamma). How could I proceed?

genome ensembl coordinates bed • 1.9k views
ADD COMMENTlink written 6.9 years ago by Anima Mundi2.4k
2
gravatar for Leszek
6.9 years ago by
Leszek4.0k
IIMCB, Poland
Leszek4.0k wrote:

Have you tried biomart? I think this is what you are looking for:)

ADD COMMENTlink written 6.9 years ago by Leszek4.0k

Thank you too, Leszek.

ADD REPLYlink written 6.9 years ago by Anima Mundi2.4k
2
gravatar for Leonor Palmeira
6.9 years ago by
Leonor Palmeira3.7k
Liège, Belgium
Leonor Palmeira3.7k wrote:

I would try either:

  • BioMart: asking to get all mouse genes (+Description+Start+End), then parse the output to create a BED format containing only 'tubulin' genes with their positions on the genome.

or

  • UCSC Genome Browser: ask to output all mouse genes (say RefSeq Genes), then retrieve complete annotations corresponding to all accession numbers (http://www.ncbi.nlm.nih.gov/sites/batchentrez). Parse both these files to create your final BED file.
ADD COMMENTlink written 6.9 years ago by Leonor Palmeira3.7k

This is what I did, thank you!

ADD REPLYlink written 6.9 years ago by Anima Mundi2.4k
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