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Retrieve Genomic Ranges From Ensembl Genomes Using Gene Names

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?

ensembl genome coordinates bed
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updated by Leonor Palmeira Leonor Palmeira • written by Anima Mundi Anima Mundi

2 answers

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

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written by Leszek Leszek

Thank you too, Leszek.

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written by Anima Mundi Anima Mundi

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.
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written by Leonor Palmeira Leonor Palmeira

This is what I did, thank you!

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written by Anima Mundi Anima Mundi

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