IMPORTANT: As of February 4, 2020, the BLAST databases on the FTP site are version 5 (v5).
At the same time, the databases offered has been changed. This document reflects those changes.
Information on newly enabled features with the v5 databases at
https://ftp.ncbi.nlm.nih.gov/blast/db/blastdbv5.pdf

This document describes the BLAST databases available on the NCBI FTP site under
the /blast/db directory. The direct URL is ftp://ftp.ncbi.nlm.nih.gov/blast/db

1. Quick Start

   • Get all numbered files for a database with the same base name:
     Each of these files represents a subset (volume) of that database,
     and all of them are needed to reconstitute the database.
   • After extraction, there is no need to concatenate the resulting files:
     Call the database with the base name, for nr database files, use "-db nr".
   • For easy download, use the update_blastdb.pl script from the blast+ package.
   • Incremental update is not available.

2. General Introduction

BLAST search pages under the Basic BLAST section of the NCBI BLAST home page
(http://blast.ncbi.nlm.nih.gov/) use a standard set of BLAST databases for
nucleotide, protein, and translated BLAST searches. These databases are made
available as compressed archives of pre-formatted form) and can be downloaded from
the /db directory of the BLAST ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/db/).
The FASTA files reside under the /FASTA subdirectory.

The pre-formatted databases offer the following advantages:
* Pre-formatting removes the need to run makeblastdb;
* Species-level taxonomy ids are included for each database entry;
* Databases are broken into smaller-sized volumes and are therefore easier
to download;
* Sequences in FASTA format can be generated from the pre-formatted databases
by using the blastdbcmd utility;
* A convenient script (update_blastdb.pl) is available in the blast+ package
to download the pre-formatted databases.

Pre-formatted databases must be downloaded using the update_blastdb.pl script or
via FTP in binary mode. Documentation for this script can be obtained by running
the script without any arguments; Perl installation is required.

The compressed files downloaded must be inflated with gzip or other decompress
tools. The BLAST database files can then be extracted out of the resulting tar
file using the tar utility on Unix/Linux, or WinZip and StuffIt Expander on
Windows and Macintosh platforms, respectively.

Large databases are formatted in multiple one-gigabyte volumes, which are named
using the basename.##.tar.gz convention. All volumes with the same base name are
required. An alias file is provided to tie individual volumes together so that
the database can be called using the base name (without the .nal or .pal
extension). For example, to call the est database, simply use "-db est" option
in the command line (without the quotes).

For other genomic BLAST databases, please check the genomes ftp directory at:
ftp://ftp.ncbi.nlm.nih.gov/genomes/

3. Contents of the /blast/db/ directory

The pre-formatted BLAST databases are archived in this directory. The names of
the available databases are listed at https://github.com/ncbi/blast_plus_docs#blast-databases
It is recommended to use update_blastdb.pl to download databases from the FTP site in order to make
sure that all volumes are downloaded.

4. Contents of the /blast/db/FASTA directory

This directory contains FASTA formatted sequence files. The file names
and database contents are listed below. These files must be unpacked before
use. They are provided as a convenience for users needing these sets in
FASTA format. For use with BLAST, it is preferable to use the BLAST database
on the FTP site.

+-----------------------+-----------------------------------------------------+
|File Name | Content Description |
+-----------------------+-----------------------------------------------------+
nr.gz* | non-redundant protein sequence database with entries
from GenPept, Swissprot, PIR, PDF, PDB, and RefSeq
nt.gz* | nucleotide sequence database, with entries from all
traditional divisions of GenBank, EMBL, and DDBJ;
excluding bulk divisions (gss, sts, pat, est, htg)
and wgs entries. Partially non-redundant.
pdbaa.gz* | protein sequences from pdb protein structures
swissprot.gz* | swiss-prot database (last major release)
+-----------------------+---------------------------------------------------+
NOTE:
(1) For screening for vector contamination, use the UniVec database:
ftp://ftp.ncbi.nlm.nih.gov/pub/UniVec/

• marked files have pre-formatted counterparts.

5. Database updates

The BLAST databases are updated regularly. There is no established incremental
update scheme. We recommend downloading the complete databases regularly to
keep their content current.

6. Non-redundant defline syntax

The non-redundant databases are nr, nt and pataa. Identical sequences are
merged into one entry in these databases. To be merged two sequences must
have identical lengths and every residue at every position must be the
same. The FASTA deflines for the different entries that belong to one
record are separated by control-A characters invisible to most
programs. In the example below both entries Q57293.1 and AAB05030.1
have the same sequence, in every respect:

Q57293.1 RecName: Full=Fe(3+) ions import ATP-binding protein FbpC ^AAAB05030.1 afuC
[Actinobacillus pleuropneumoniae] ^AAAB17216.1 afuC [Actinobacillus pleuropneumoniae]
MNNDFLVLKNITKSFGKATVIDNLDLVIKRGTMVTLLGPSGCGKTTVLRLVAGLENPTSGQIFIDGEDVTKSSIQNRDIC
IVFQSYALFPHMSIGDNVGYGLRMQGVSNEERKQRVKEALELVDLAGFADRFVDQISGGQQQRVALARALVLKPKVLILD
EPLSNLDANLRRSMREKIRELQQRLGITSLYVTHDQTEAFAVSDEVIVMNKGTIMQKARQKIFIYDRILYSLRNFMGEST
ICDGNLNQGTVSIGDYRFPLHNAADFSVADGACLVGVRPEAIRLTATGETSQRCQIKSAVYMGNHWEIVANWNGKDVLIN
ANPDQFDPDATKAFIHFTEQGIFLLNKE

Individual sequences are now identified simply by their accession.version.

For databases whose entries are not from official NCBI sequence databases,
such as Trace database, the gnl| convention is used. For custom databases,
this convention should be followed and the id for each sequence must be
unique, if one would like to take the advantage of indexed database,
which enables specific sequence retrieval using blastdbcmd program included
in the blast executable package. One should refer to documents
distributed in the standalone BLAST package for more details.

7. Formatting a FASTA file into a BLASTable database

FASTA files need to be formatted with makeblastdb before they can be used in local
blast search. For those from NCBI, the following makeblastdb commands are
recommended:

For nucleotide fasta file: makeblastdb -in input_db -dbtype nucl -parse_seqids
For protein fasta file: makeblastdb -in input_db -dbtype prot -parse_seqids

In general, if the database is available as BLAST database, it is better to use the
preformatted database.

8. Technical Support

Questions and comments on this document and NCBI BLAST related questions
should be sent to the blast-help group at:
blast-help@ncbi.nlm.nih.gov

For information about other NCBI resources/services, please send email to
NCBI User Service at:
info@ncbi.nlm.nih.gov