Entering edit mode
8.0 years ago
mirza
▴
180
Hi,
I am trying to search the whole genome sequences (assembled) of some specific varieties of rice. For this, I am exploring the 3000 rice genome project, both the ebi and ncbi link (ddbj link is not working) but can't figure it out. Can anyone help?
From the EBI-ENA page you can download the read files and should get what you are looking for. I guess the best thing about sequencing some many genomes is discovering genetic variants (SNPs, CNVs, etc) and this variation data will be soon in Ensembl Plants. At the moment we've got already data for more than 10 Oryza sp (genomic sequence, variation data, GO annotation, protein family annotation, etc) but more is to come. Watch this space.
Thank you Denise for your reply. I was looking for assembled genome sequences for some rice varieties and could only see the reads files there so didn't download it.
I see. Perhaps it's worth contacting the names for contact within the consortium, which are listed here [1]? Not sure if assembled sequences are available out there but Zhang et al would be the best people to confirm this, I'd have thought.
Thanks for the suggestion Denise. That would have been the best thing to do but unfortunately, my rice varieties are not there in the list, I checked.