Hi all, Now I'm trying to get fasta file of CDSs (with protein) on the genome, but I have no idea which data to use. What is the difference between the data obtained from 1 and 2? I want to use RefSeq data.
Thank you in advance.
Multiple ways to do this;
If you want protein sequence: $ esearch -db nuccore -query NC_018025 | elink -target protein | efetch -format fasta > protein.fa
genome or protein links in the screenshot you posted above)Visit : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/266/945/GCF_000266945.1_ASM26694v1/
Get Nucleotide CDS: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/266/945/GCF_000266945.1_ASM26694v1/GCF_000266945.1_ASM26694v1_cds_from_genomic.fna.gz
Get Protein Sequence: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/266/945/GCF_000266945.1_ASM26694v1/GCF_000266945.1_ASM26694v1_protein.faa.gz
You can also use NCBI Datasets tool: https://www.ncbi.nlm.nih.gov/data-hub/taxonomy/706587/
Search for your genome at: https://www.ncbi.nlm.nih.gov/datasets/ I provided a direct link above.
Thank you very much. If I download faa.gz file of this genome from the NCBI FTP site, does this file contain the protein sequences from both NC_018025.1 and NC_018026.1?
Looks like it.
$ zgrep "^>" GCF_000266945.1_ASM26694v1_protein.faa.gz | wc -l
5199
Using EntrezDirect on individual accessions yields
$ esearch -db nuccore -query NC_018025 | elink -target protein | efetch -format fasta | grep ">" | wc -l
5176
$ esearch -db nuccore -query NC_018026 | elink -target protein | efetch -format fasta | grep ">" | wc -l
23
Thank you so much! Now I understand how it works.
You already found some files, but here is a general approach to finding genomic assemblies. From the main NCBI site:
In the search box we type the organism of interest, and in search results we select Assembly. In your case there are 6 of them, so you pick whichever you like best. I am going with Desulfomonile tiedjei DSM 6799.
https://www.ncbi.nlm.nih.gov/assembly/?term=desulfomonile%20tiedjei
On the right-hand side you click on "FTP for RefSeq assembly". From that directory you want a file that ends in .faa.gz for protein translation.
The README file explains what the others are.
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Which genome? What is 1 and 2? Please provide accession number example.
Sorry I forgot to attach the image.