Retrieve Genomic Ranges From Ensembl Genomes Using Gene Names

Question

[Anima Mundi]

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?

Answer 1

[Leszek]

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

[Anima Mundi]

Thank you too, Leszek.

Answer 2

[Leonor Palmeira]

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.

[Anima Mundi]

This is what I did, thank you!