Acquiring Fasta files for a custom database

Question

[danielcastillo2101037]

Hello, I am interested in Blasting against a custom database of about 100 bacterial genomes. First, I was wondering if someone might be able to suggest a method of downloading the annotated genomes from NCBI or some other source without having to download each file on the command line one by one. Unfortunately, they are not consolidated in once place. For each organism I have the IMG Genome ID. I understand how to make the custom database, but do not know how to get the necessary fasta files. Best and thank you.

[GenoMax]

See @5heikki's receipe for downloading bacterial genomes from NCBI in this thread. Modify as needed.: C: Download All The Bacterial Genomes From Ncbi

Answer 1

[natasha.sernova]

See my answer inside this post

where can I get environmental bacteria genome in fasta format (as many as possible)?

and pay attention to old NCBI-site copy.

ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/

You will find *.gz-files there for all the bacteria.

This version is about 2 years old, but most bacterial genomes were deposited there much earlier.

If you have some doubts, you can always compare with current

NCBI-links, they were also mentioned in this post. where can I get environmental bacteria genome in fasta format (as many as possible)?