Regarding Barley genome

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4.0 years ago

umeshtanwar2 ▴ 30

Hi all, I have recently started working with Barley (Hordeum vulgare) plant - Cultivar Golden Promise. I am interested in some genes and I got their CDS from https://webblast.ipk-gatersleben.de/barley_ibsc/viroblast.php database. But I could not find the genomic sequence. My questions are:

How to find the genomic sequences?
There is recently an article published: A Genome Assembly of the Barley ‘Transformation Reference’ Cultivar Golden Promise (https://www.g3journal.org/content/10/6/1823). Can I use this genome assembly? If yes, how can I use this to find the genomic sequences?

Thank you Umesh

Assembly gene genome • 819 views

ADD COMMENT • link 4.0 years ago by umeshtanwar2 ▴ 30

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You may want to grab genome sequence from Ensembl. You can find the genome sequence and CDS from this FTP location.

ADD REPLY • link 4.0 years ago by GenoMax 147k

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Thank you so much. Can you please also suggest any tools that I can use to extract the sequence of my gene of interest.

ADD REPLY • link 4.0 years ago by umeshtanwar2 ▴ 30

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use the BioMart https://plants.ensembl.org/biomart/martview

ADD REPLY • link 4.0 years ago by JC 13k

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If you get the CDS file (and know the ID of the gene you are interested in) you can find the sequence of the gene. Note these don't contain introns or UTR sequences.