The BLAST Databases
Last updated on October 2, 2008
This document describes the "BLAST" databases available on the NCBI
FTP site under the /blast/db directory. The direct URL is:
ftp://ftp.ncbi.nih.gov/blast/db
1. General Introduction
NCBI BLAST home pages (http://www.ncbi.nih.gov/BLAST/) use a standard
set of BLAST databases for Nucleotide, Protein, and Translated BLAST
searches. These databases are made available in the /blast/db directory as
compressed archives (ftp://ftp.ncbi.nih.gov/blast/db/) in pre-formatted
format. The FASTA databases reside under the /blast/db/FASTA directory.
The pre-formatted databases offer the following advantages:
* The pre-formatted databases are smaller in size and therefore are
faster to download;
* Sequences in FASTA format can be generated from the pre-formatted
databases by the fastacmd utility;
* A convenient script (update_blastdb.pl) is available to download
the pre-formatted databases from the NCBI ftp site;
* Pre-formatting removes the need to run formatdb;
* Taxonomy ids are available for each database entry.
Pre-formatted databases must be downloaded using the update_blastdb.pl
script or via FTP in binary mode. Documentation for the update_blastdb.pl
script can be obtained by running the script without any arguments (perl 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 tar program on Unix/Linux or WinZip and StuffIt Expander
on Windows and Macintosh platforms, respectively.
Large databases are formatted in multiple 1 Gigabytes volumes, which
are named using the database.##.tar.gz convention. All relevant volumes
are required. An alias file is provided so that the database can be called
using the alias name without the extension (.nal or .pal). For example,
to call est database, simply use "-d est" option in the commandline
(without the quotes).
Certain databases are subsets of a larger parental database. For those
databases, alias and mask files, rather than actual databases, are provided.
The mask file needs the parent database to function properly. The parent
databases should be generated on the same day as the mask file. For
example, to use swissprot pre-formatted database, swissprot.tar.gz, one
will need to get the nr.tar.gz with the same date stamp.
Additional BLAST databases that are not provided in pre-formatted
formats are available in the FASTA subdirectory. For genomic BLAST
databases, please check the genomes ftp directory at:
ftp://ftp.ncbi.nih.gov/genomes/
2. Contents of the /blast/db/ directory
The pre-formatted BLAST databases are archived in this directory. The
name of these databases and their contents are listed below.
+----------------------+-----------------------------------------------+
|File Name | Content Description |
+----------------------+-----------------------------------------------+
/FASTA | subdirectory for FASTA formatted sequences
README | README for this subdirectory (this file)
env_nr.*tar.gz | Environmental protein sequences
env_nt.*tar.gz | Environmental nucleotide sequences
est.*tar.gz | volumes of the formatted est database
| from the EST division of GenBank, EMBL,
| and DDBJ
est_human.tar.gz | alias and mask files for human subset of the est
est_mouse.tar.gz | alias and mask files for mouse subset of the est
est_others.tar.gz | alias and mask files for non-human and non-mouse
| subset of the est database
| These alias and mask files need all volumes of
| est to function properly.
gss.*tar.gz | volumes of the formatted gss database
| from the GSS division of GenBank, EMBL, and
| DDBJ
htgs.*tar.gz | volumes of htgs database with entries0tifiers) in a
file. One can obtain a list of gi's for a given Entrez query from
http://www.ncbi.nlm.nih.gov/Entrez/batch.html. This file should
be in the same directory as the database, or in the directory that
BLAST is called from.
-U Use lower case filtering of FASTA sequence [T/F] Optional
default = F
This option specifies that any lower-case letters in the input FASTA file
should be masked.
Enhancements:
A new option has been added to search multiple queries at once for the
blastn and tblastn program options of blastall.
-B Number of concatenated queries, for blastn and tblastn [Integer]
Optional
default = 0
This new feature similar in principle, but different in implementation
from the support for multiple queries already existing in megablast.
The combination of ungapped search (-g F) and multiple queries
(-B N) is not supported. The argument to -B option must be equal
to the number of sequences in the FASTA input file.
Processing multiple query sequences in one run can be much faster than
processing them with separate runs because the database is scanned only 1
time for the entire set of queries. When the -B option is used, the
results may differ from the ones produced with individual queries. Usually
results will be at least as good or better (in terms of score/evalue)
than the results of corresponding individual queries; exceptions occur
due to the heuristic nature of BLAST. Additional alignments may appear.
It is guaranteed that matching sequences will
appear in the same order when they are tied in evalue
and are part of the output both with and without -B.
When the -B option is used, the summary statistics at the bottom
of the output are for the combined set of queries; at present,
the summary statistics are not tabulated for the individual
queries in a multiple-query input.