The BLAST Databases
Last updated on January 12, 2015
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重建 the database.
* After extraction, there is no need to concatenate连接 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增加 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压缩 archives文档 of pre-formatted form) and can be donwloaed from
the /db directory of the BLAST ftp site (ftp://ftp.ncbi.nlm.nih.gov/blast/db/).
The FASTA files reside位于 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版本, which are named
using the basename.##.tar.gz convention习俗. 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).
Additional BLAST databases that are not provided in pre-formatted formats may
be available in the FASTA subdirectory. 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
these databases and their contents are listed below.
+-----------------------------+------------------------------------------------+
File Name | Content Description
+-----------------------------+------------------------------------------------+
16SMicrobial.tar.gz | Bacterial and Archaeal 16S rRNA sequences from
BioProjects 33175 and 33117
FASTA/ | Subdirectory for FASTA formatted sequences
README | README for this subdirectory (this file)
Representative_Genomes.*tar.gz| Representative典型 bacterial/archaeal genomes database
cdd_delta.tar.gz | Conserved保守 Domain Database sequences for use with
stand alone deltablast
cloud/ | Subdirectory of databases for BLAST AMI; see
http://1.usa.gov/TJAnEt
env_nr.*tar.gz | Protein sequences for metagenomes
env_nt.*tar.gz | Nucleotide sequences for metagenomes
est.tar.gz | This file requires est_human.*.tar.gz,
est_mouse.*.tar.gz, and est_others.*.tar.gz files
to function. It contains the est.nal alias so that
searches against est (-db est) will include
est_human, est_mouse and est_others.
est_human.*.tar.gz | Human subset of the est表达序列标签 database from the est
division of GenBank, EMBL and DDBJ.
est_mouse.*.tar.gz | Mouse subset of the est databasae
est_others.*.tar.gz | Non-human and non-mouse subset of the est database
gss.*tar.gz | Sequences from the GSS division of GenBank,
EMBL, and DDBJ基因勘测序列
htgs.*tar.gz | Sequences from the HTG division of GenBank, EMBL,
and DDBJ
human_genomic.*tar.gz | Human RefSeq (NC_######) chromosome records with
gap adjusted concatenated NT_ contigs
nr.*tar.gz | Non-redundant protein sequences from GenPept,
Swissprot, PIR, PDF, PDB, and NCBI RefSeq
nt.*tar.gz | Partially non-redundant nucleotide sequences from
all traditional divisions of GenBank, EMBL, and DDBJ
excluding GSS,STS, PAT, EST, HTG, and WGS.
other_genomic.*tar.gz | RefSeq chromosome records (NC_######) for non-human
organisms
pataa.*tar.gz | Patent protein sequences
patnt.*tar.gz | Patent nucleotide sequences. Both patent databases
are directly from the USPTO, or from the EPO/JPO
via EMBL/DDBJ
pdbaa.*tar.gz | Sequences for the protein structure from the
Protein Data Bank
pdbnt.*tar.gz | Sequences for the nucleotide structure from the
Protein Data Bank. They are NOT the protein coding
sequences for the corresponding pdbaa entries.
refseq_genomic.*tar.gz | NCBI genomic reference sequences
refseq_protein.*tar.gz | NCBI protein reference sequences
refseq_rna.*tar.gz | NCBI Transcript reference sequences
sts.*tar.gz | Sequences from the STS division of GenBank, EMBL,
and DDBJ序列标签位点
swissprot.tar.gz | Swiss-Prot sequence database (last major update)
taxdb.tar.gz | Additional taxonomy information for the databases
listed here
| providing common and scientific names
tsa_nt.*tar.gz | Sequences from the TSA division of GenBank, EMBL,
and DDBJ
vector.tar.gz | Vector sequences from 2010, see Note 2 in section 4.
wgs.*tar.gz | Sequences from Whole Genome Shotgun assemblies
+-----------------------------+------------------------------------------------+
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非压缩 and
processed through blastdbcmd建库命令 before they can be used by the BLAST programs.
+-----------------------+-----------------------------------------------------+
|File Name | Content Description |
+-----------------------+-----------------------------------------------------+
alu.a.gz | translation of alu.n repeats
alu.n.gz | alu repeat elements (from 2003)
drosoph.aa.gz | CDS translations from drosophila.nt
drosoph.nt.gz | genomic sequences for drosophila (from 2003)
env_nr.gz* | Protein sequences for metagenomes, taxid 408169
env_nt.gz* | Nucleotide sequences for metagenomes, taxid 408169
est_human.gz* | human subset of the est database (see Note 1)
est_mouse.gz* | mouse subset of the est database
est_others.gz* | non-human and non-mouse subset of the est database
gss.gz* | sequences from the GSS division of GenBank, EMBL,
and DDBJ
htgs.gz* | sequences from the HTG division of GenBank, EMBL,
and DDBJ
human_genomic.gz* | human RefSeq (NC_######) chromosome records
with gap adjusted concatenated NT_ contigs
igSeqNt.gz | human and mouse immunoglobulin variable region
nucleotide sequences
igSeqProt.gz | human and mouse immunoglobulin variable region
protein sequences
mito.aa.gz | CDS translations of complete mitochondrial genomes
mito.nt.gz | complete mitochondrial genomes
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.
other_genomic.gz* | RefSeq chromosome records (NC_######) for organisms
other than human
pataa.gz* | patent protein sequences
patnt.gz* | patent nucleotide sequences. Both patent sequence
files are from the USPTO, or EPO/JPO via EMBL/DDBJ
pdbaa.gz* | protein sequences from pdb protein structures
pdbnt.gz* | nucleotide sequences from pdb nucleic acid
structures. They are NOT the protein coding
sequences for the corresponding pdbaa entries.
sts.gz* | database for sequence tag site entries
swissprot.gz* | swiss-prot database (last major release)
vector.gz | vector sequences from 2010. (See Note 2)
wgs.gz* | whole genome shotgun genome assemblies
yeast.aa.gz | protein translations from yeast.nt
yeast.nt.gz | yeast genomes (from 2003)
+-----------------------+---------------------------------------------------+
NOTE:
(1) NCBI does not provide the complete est database in FASTA format. One
needs to get all three subsets (est_human, est_mouse, and est_others
and concatenate them into the complete est fasta database).
(2) 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增加的
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 (partially) and pataa. In them,
identical sequences are merged into one entry. 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 gi|1469284 and gi|1477453
have the same sequence, in every respect:
>gi|3023276|sp|Q57293|AFUC_ACTPL Ferric transport ATP-binding protein afuC
^Agi|1469284|gb|AAB05030.1| afuC gene product ^Agi|1477453|gb|AAB17216.1|
afuC [Actinobacillus pleuropneumoniae]
MNNDFLVLKNITKSFGKATVIDNLDLVIKRGTMVTLLGPSGCGKTTVLRLVAGLENPTSGQIFIDGEDVT
KSSIQNRDICIVFQSYALFPHMSIGDNVGYGLRMQGVSNEERKQRVKEALELVDLAGFADRFVDQISGGQ
QQRVALARALVLKPKVLILDEPLSNLDANLRRSMREKIRELQQRLGITSLYVTHDQTEAFAVSDEVIVMN
KGTIMQKARQKIFIYDRILYSLRNFMGESTICDGNLNQGTVSIGDYRFPLHNAADFSVADGACLVGVRPE
AIRLTATGETSQRCQIKSAVYMGNHWEIVANWNGKDVLINANPDQFDPDATKAFIHFTEQGIFLLNKE
The syntax of sequence header lines used by the NCBI BLAST server depends on
the database from which each sequence was obtained. The table at
http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_demo/?report=objectonly#ch_demo.T5
lists the supported FASTA identifiers.
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检索 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建库 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
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
