eukaryotic genome databases

Question

[Mero]

Hello!

Do you know any databases that I can download eukaryotic genome fasta file for each different eukaryotic species separately? For example if I have 3 different species I want 3 fasta files for of them that contains their genome. Since I am new to all of this, even though I looked for ncbi couldn't find what I wanted. A little help would be appreciated.

Thank you!

Answer 1

[GenoMax]

You can use NCBI genome datasets tool as an easy option. Here is an example of Pseudomonas aeruginosa strains page (search with your own organism when you do this for real) : https://ncbi.nlm.nih.gov/datasets/genome/?taxon=287 or if you prefer Arabidopsis is an eukaryotic example: https://ncbi.nlm.nih.gov/datasets/genome/?taxon=3702

You can then click on any strain you want. That will open the strain specific page. On that page there is a Download button. Once you click that it will give you options for things you can download. Select genome fasta (and anything else you need).

Then click the final Download button to download the file as a zip archive. All files are called "ncbi_datasets.zip` so rename as necessary.

Note: Datasets tool can also be used on the command line if you are comfortable with unix.

Answer 2

[Pierre Lindenbaum]

Have a look at Ensembl or ucsc genark https://genome-blog.gi.ucsc.edu/blog/2021/11/23/genark-hubs-part-1/