The NCBI RefSeq files can be downloaded for all species from the NCBI RefSeq FTP Site - https://ftp.ncbi.nlm.nih.gov/refseq/

Files (all) related to proteins are downloaded from the FTP site in the downloads folder in the GlyGen Dev server such as -
.protein.faa.gz
.protein.gpff.gz

For homo sapiens - ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/
For mus musculus - ftp://ftp.ncbi.nlm.nih.gov/refseq/M_musculus/mRNA_Prot/
For rattus norvegicus - ftp://ftp.ncbi.nlm.nih.gov/refseq/R_norvegicus/mRNA_Prot/
For virus (all) - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/
For Dictyostelium discoideum - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/protozoa/
For Sus scrofa - ftp://ftp.ncbi.nlm.nih.gov/refseq/release/vertebrate_mammalian/

Make sure the path is ftp://ftp.ncbi.nlm... and not 'https://ftp.ncbi.nlm.' in the script

Check the script at data/projects/glygen/downloads/download_scripts/download_refseq.sh has the information of files for new organism

In the /download_scripts, run the script to download all the files:
bash download_refseq.sh

Go to downloads/ncbi/refseq/ and check the newly created folder with all downloaded and unzipped contents.

Make sure the new folder with new data has been marked as current and that the symbolic link was created successfully. Create a ticket for Robel to update the files. 
If any new changes have been found notify him. Make necessary changes to the files in misc folder and ifneeded.
Reflect any new changes in BCOs

Robel will be processing the below files
refseq_protein_all_9606.faa
refseq_protein_all_9606.gpff
refseq_protein_all_10090.faa
refseq_protein_all_10090.gpff
refseq_protein_all_10116.faa
refseq_protein_all_10116.gpff
refseq_protein_all_viral.faa
refseq_protein_all_viral.gpff
refseq_protein_all_7227.gpff
refseq_protein_all_7227.faa
refseq_protein_all_559292.gpff
refseq_protein_all_559292.faa
refseq_protein_all_44689.gpff
refseq_protein_all_44689.faa
refseq_protein_all_9823.gpff
refseq_protein_all_9823.faa

Make sure to update the script when a new organism is added, for future releases. 

last edited by Jingyue on Jan 31, 2024