NCBI DB and Taxonomy classification

Question

[Giulia.cosenza]

Hi, I'd like to perform a taxonomic classification (not only of microorganisms but also of all Eukaryota) of shotgun output sequences with megan6, which requires to download a reference db with sequences or genomes to compare. I was looking for something usefull in the Index of /blast/db (nih.gov) site but I couldn't understand the differences between some file such as:

• the 82 nt.XX.tar.gz files in the ftp://ftp.ncbi.nlm.nih.gov/blast/db/ directory and the nt.gz file in the ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA subdirectory
• the 73 nr.XX.tar.gz files in the ftp://ftp.ncbi.nlm.nih.gov/blast/db/ directory and the nr.gz file in the ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA subdirectory

Does anyone know if they are the same DBs but merged in the FASTA subdir?

Can somebody give me some help and/or advice to complete my task?

Thank you very much

Giulia 

Answer 1

[GenoMax]

Files in FASTA directory are just fasta format files for nt.

You should download the pre-formatted database files (all nt pieces) from https://ftp.ncbi.nih.gov/blast/db/.

To do taxonomy based searches you will also need a companion taxonomy database set of files. They are in the directory above with basename taxdb*. Download and have them available in the same folder as your nt files.