The BLAST Databases
Last updated on August 4, 2005
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 entries
| from 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 sequence database with
| entries from GenPept, Swissprot, PIR, PDF, PDB,
| and NCBI RefSeq
nt.*tar.gz | nucleotide sequence database, with entries
| from all traditional divisions of GenBank,
| EMBL, and DDBJ excluding bulk divisions (gss,
| sts, pat, est, and htg divisions. wgs entries
| are also excluded. Not non-redundant.
other_genomic.*tar.gz | RefSeq chromosome records (NC_######) for
| organisms other than human
pataa.*tar.gz | patent protein sequence database
patnt.*tar.gz | patent nucleotide sequence database
| The above two databases are directly from
| USPTO or from EU/Japan Patent Agencies via
| EMBL/DDBJ
pdbaa.*tar.gz | protein sequences from pdb protein structures,
| its parent database is nr.
pdbnt.*tar.gz | nucleotide sequences from pdb nucleic acid
| structures, its parent database it nt. 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
swissprot.tar.gz | swiss-prot sequence databases (last major update),
| its parent database is nr.
taxdb.tar.gz | Additional taxonomy information for the formatted
| database (contains common and scientific names)
wgs.*tar.gz | volumes for whole genome shotgun sequence assemblies
| for different organisms
+----------------------+-----------------------------------------------+
3. 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 are now archived
in .gz format and must be processed through formatdb 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
drosoph.aa.gz | CDS translations from drosophila.nt
drosoph.nt.gz | genomic sequences for drosophila
ecoli.aa.gz | CDS translations from ecoli.nt
ecoli.nt.gz | Escherichia coli K-12 genomic sequences
env_nr.gz* | Environmental protein sequences
env_nt.gz* | Environmental nucleotide sequences
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
htg.gz* | htgs database with high throughput genomic
| entries 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 nucleotide
| sequences
igSeqProt.gz | human and mouse immunoglobulin protein
| sequences
mito.aa.gz | CDS translations of complete mitochondrial
| genomes
mito.nt.gz | complete mitochondrial genomes
month.aa.gz | newly released/updated protein sequences
(See Note 2)
month.est_human.gz | newly released/updated human est sequences
month.est_mouse.gz | newly released/updated mouse est sequences
month.est_others.gz | newly released/updated est other than
| human/mouse
month.gss.gz | newly released/updated gss sequences
month.htgs.gz | newly released/updated htgs sequences
month.nt.gz | newly released/updated sequences for the nt
database
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 divisions) and wgs
| entries. Not non-redundant.
other_genomic.gz* | RefSeq chromosome records (NC_######) for
| organisms other than human
pataa.gz* | patent protein sequence database
patnt.gz* | patent nucleotide sequence database
| The above two dbs are directly from USPTO
| of from EU/Japan Patent Agency 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 sequence database (See Note 3)
wgs.gz* | whole genome shotgun genome assemblies
yeast.aa.gz | protein translations from yeast genome
yeast.nt.gz | yeast genomes.
+-----------------------+-----------------------------------------------+
NOTE:
(1) we do not provide the complete est database in FASTA format. One
need to get all three subsets(est_human, est_mouse, and est_others
and concatenate them into the complete est fasta database.
(2) month.### databases are the sequences newly released or updated
within the last 30 days for that database.
(3) For vector contamination screening, use the UniVec database from:
ftp://ftp.ncbi.nih.gov/pub/UniVec/
* marked files have pre-formatted counterparts.
4. Database updates
The BLAST databases are updated daily. Update of existing databases
by merging of new records from the month database using fmerge is no
longer supported. We do not have an established incremental update
scheme at this time. We recommend downloading the databases regularly
to keep their content current.
5. Non-redundant defline syntax
The only non-redundant databases are nr (and its subsets) 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
nr 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
below lists the identifiers for the databases from which the sequences
were derived.
Database Name Identifier Syntax
============================ ========================
GenBank gb|accession|locus
EMBL Data Library emb|accession|locus
DDBJ, DNA Database of Japan dbj|accession|locus
NBRF PIR pir||entry
Protein Research Foundation prf||name
SWISS-PROT sp|accession|entry name
Brookhaven Protein Data Bank pdb|entry|chain
Patents pat|country|number
GenInfo Backbone Id bbs|number
General database identifier gnl|database|identifier
NCBI Reference Sequence ref|accession|locus
Local Sequence identifier lcl|identifier
"gi" identifiers are being assigned by NCBI for all sequences contained
within NCBI's sequence databases. The "gi" identifier provides a uniform
and stable naming convention whereby a specific sequence is assigned its
unique gi identifier. If a nucleotide or protein sequence changes,
however, a new gi identifier is assigned, even if the accession number
of the record remains unchanged. Thus gi identifiers provide a mechanism
for identifying the exact sequence that was used or retrieved in a given
search.
We recommend that "gi display option" be activated in local blast search
by setting the -I option to T, which was set to false by default:
-I Show GI's in deflines [T/F]
default = F
For databases whose entries are not from official NCBI sequence databases,
such as Trace database, the gnl| convention is used. For custom database,
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 fastacmd program included
in the blast executable package. One should refer to documents
distributed in the standalone BLAST package for more details.
6. Formatting the FASTA database
FASTA database files need to be formatted with formatdb before they can be
used in local blast search. For those from NCBI, the following formatdb
are recommended:
formatdb -i input_db -p F -o T for nucleotide
formatdb -i input_db -p T -o T for protein
The -A option introduced in 2.2.3 is now built into the formatdb program
and thus removed from the list of configurable options since 2.2.8. This
enables formatdb to properly handle large sequence files (longer than 16
million bases). Please refer to formatdb.html under the /blast/documents
directory for more information. Databases prepared using 2.2.8 formatdb
will not be backward compatible with blast programs old than version 2.2.3.
7. Technical Support
Questions and comments on this document and NCBI BLAST related questions
should be sent to 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