Question: Regarding Barley genome
0
gravatar for umeshtanwar2
8 weeks ago by
umeshtanwar220
umeshtanwar220 wrote:

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:

  1. How to find the genomic sequences?
  2. 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

genome assembly gene • 131 views
ADD COMMENTlink written 8 weeks ago by umeshtanwar220
1

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

ADD REPLYlink written 8 weeks ago by GenoMax95k

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 REPLYlink written 8 weeks ago by umeshtanwar220

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

ADD REPLYlink written 8 weeks ago by JC12k

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.

ADD REPLYlink written 8 weeks ago by GenoMax95k

Thank you genomax and JC.

ADD REPLYlink written 8 weeks ago by umeshtanwar220
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