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Last updated on July 21, 2003
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This document describes the "BLAST" databases available on the NCBI
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FTP site under the "blast/db" subdirectory. The direct URL to this
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ftp://ftp.ncbi.nih.gov/blast/db
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I. General Introduction
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NCBI BLAST home pages (http://www.ncbi.nih.gov/BLAST/) use a standard
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set of BLAST databases for Nucleotide, Protein, and Translated BLAST
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searches. These databases are made available in the db directory as
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compressed archives (ftp://ftp.ncbi.nih.gov/blast/db/) in preformatted
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format. The FASTA databases now reside under the blast/FASTA
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The preformatted databases offer the following advantages:
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* The preformatted databases are smaller in size and are
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* Preformatting removes the need to run formatdb;
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* Taxonomy information is available for each database entry.
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Preformatted databases must be downloaded in binary mode and inflated
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with gzip or other decompress tools. The BLAST database files can then
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be extracted out of the resulting tar file using �tar� program on Unix/Linux
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or WinZip and StuffIt Expander on Windows and Macintosh platforms,
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Large databases are formatted in multiple 1 Gigabytes volumes, which
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are named using the �database.##.tar.gz� convention. All relevant volumes
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are required. An alias file is provided so that the database can be called
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using the alias name without the extension (.nal or .pal). For example,
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to call est database, simply use ��d est� option in the commandline
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Certain databases are subsets of a larger parental database. For those
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databases, mask files, rather than actual databases, are provided. The
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mask file needs the parent database to function properly. The parent
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databases should be generated on the same day as the mask file. For
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example, to use swissprot preformatted database, swissprot.tar.gz, one
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will need to get the nr.tar.gz with the same date stamp.
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Additional BLAST databases that are not provided in preformatted
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formats are available in the FASTA subdirectory. For genomic BLAST
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databases, please check the genomes ftp directory at:
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ftp://ftp.ncbi.nih.gov/genomes/
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2. Contents of the /blast/db/ directory
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The formatted databases are archived in this directory. The name of
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these databases and their contents are listed below.
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+--------------------+-----------------------------------------------+
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|File Name | Content Description |
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+--------------------+-----------------------------------------------+
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/FASTA subdirectory for FASTA formatted sequences
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README README for this subdirectory (this file)
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est.00.tar.gz | three volumes of the formatted est database
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est.01.tar.gz | from the EST division of GenBank, EMBL,
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est.02.tar.gz | and DDBJ
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est_human.tar.gz | mask file for human subset of the est
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est_mouse.tar.gz | mask file for mouse subset of the est
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est_others.tar.gz | mask file for non-human and non-mouse subset
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| These three mask files need all volumes of
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| est to function properly.
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gss.00.tar.gz | two volumes of the formatted gss database
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gss.01.tar.gz | from the GSS division of GenBank, EMBL, and
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htgs.00.tar.gz | three volumes of htgs database with entries
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htgs.01.tar.gz | from HTG division of GenBank, EMBL, and DDBJ
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human_genomic.tar.gz human RefSeq (NC_######) chromosome records
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with gap adjusted concatenated NT_ contigs
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nr.tar.gz non-redundant protein sequence database with
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entries from GenPept, Swissprot, PIR, PDF, PDB,
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nt.00.tar.gz | nucleotide sequence database, with entries
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nt.01.tar.gz | from all traditional divisions of GenBank,
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nt.02.tar.gz | EMBL, and DDBJ excluding bulk divisions (gss,
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| sts, pat, est, and htg divisions. wgs entries
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| are also excluded. Not non-redundant.
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other_genomic.tar.gz RefSeq chromosome records (NC_######) for
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organisms other than human
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pataa.tar.gz | patent protein sequence database
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patnt.tar.gz | patent nucleotide sequence database
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| The above two databases are directly from
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| USPTO or from EU/Japan Patent Agencies via
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pdbaa.tar.gz protein sequences from pdb protein structures
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pdbnt.tar.gz nucleotide sequences from pdb nucleic acid
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structures. They are NOT the protein coding
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sequences for the corresponding pdbaa entries.
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sts.tar.gz Sequences from the STS division of GenBank, EMBL,
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swissprot.tar.gz swiss-prot sequence databases (last major update)
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taxdb.tar.gz Taxonomy information for the formatted database
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wgs.00.tar.gz | Whole genome shotgun sequence assemblies for
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wgs.01.tar.gz | different organisms, broken up into 1 GB
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wgs.02.tar.gz | volumes.
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+--------------------+-----------------------------------------------+
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3. Content of the /db/FASTA Subdirectory
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This subdirectory contains FASTA formatted sequence files, formerly
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available under /db directory. The file names and database contents
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are listed below. These files are now archived in .gz format and must
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be processed through formatdb before they can be used by the BLAST
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+--------------------+-----------------------------------------------+
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|File Name | Content Description |
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+--------------------+-----------------------------------------------+
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alu.a.gz translation of alu.n repeats
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alu.n.gz alu repeat elements
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drosoph.aa.gz CDS translations from drosophila.nt
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drosoph.nt.gz genomic sequences for drosophila
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ecoli.aa.gz CDS translations from ecoli.nt
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ecoli.nt.gz Escherichia coli K-12 genomic sequences
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est_human.gz* | human subset of the est database (see Note 1)
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est_mouse.gz* | mouse subset of the est database
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est_others.gz* | non-human and non-mouse subset of the est
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gss.gz* sequences from the GSS division of GenBank,
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htg.gz* htgs database with high throughput genomic
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entries from the htg division of GenBank,
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human_genomic.gz* human RefSeq (NC_######) chromosome records
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with gap adjusted concatenated NT_ contigs
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igSeqNt.gz human and mouse immunoglobulin nucleotide
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igSeqProt.gz human and mouse immunoglobulin protein
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mito.aa.gz CDS translations of complete mitochondrial
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mito.nt.gz complete mitochondrial genomes
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month.aa.gz | newly released/updated protein sequences
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month.est_human.gz | newly released/updated human est sequences
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month.est_mouse.gz | newly released/updated mouse est sequences
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month.est_others.gz | newly released/updated est other than
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month.gss.gz | newly released/updated gss sequences
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month.htgs.gz | newly released/updated htgs sequences
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month.nt.gz | newly released/updated sequences for the nt
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nr.gz* non-redundant protein sequence database with
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entries from GenPept, Swissprot, PIR, PDF,
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nt.gz* nucleotide sequence database, with entries
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from all traditional divisions of GenBank,
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EMBL, and DDBJ excluding bulk divisions
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(gss, sts, pat, est, htg divisions) and wgs
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entries. Not non-redundant.
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other_genomic.gz* RefSeq chromosome records (NC_######) for
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organisms other than human
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pataa.gz* | patent protein sequence database
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patnt.gz* | patent nucleotide sequence database
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| The above two dbs are directly from USPTO
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| of from EU/Japan Patent Agency via EMBL/DDBJ
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pdbaa.gz* protein sequences from pdb protein structures
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pdbnt.gz* nucleotide sequences from pdb nucleic acid
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structures. They are NOT the protein coding
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sequences for the corresponding pdbaa entries.
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sts.gz* database for sequence tag site entries
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swissprot.gz* swiss-prot database (last major release)
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vector.gz vector sequence database (See Note 3)
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wgs.gz* whole genome shotgun genome assemblies
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yeast.aa.gz protein translations from yeast genome
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yeast.nt.gz yeast genomes.
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+--------------------+-----------------------------------------------+
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(1) we do not provide the complete est database in FASTA format. One
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need to get all three subsets(est_human, est_mouse, and est_others
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and concatenate them into the complete est fasta database.
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(2) month.### databases are the sequences newly released or updated
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within the last 30 days for that database.
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(3) For vector contamination screening, use the UniVec database from:
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ftp://ftp.ncbi.nih.gov/pub/UniVec/
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* marked files have preformatted counterparts.
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The BLAST databases are updated daily. Update of existing databases
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by merging of new records from the month database using fmerge is no
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longer supported. We do not have an established incremental update
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scheme at this time. We recommend downloading the databases regularly
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to keep their content current.
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5. Non-redundant defline syntax
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The only non-redundant database is the protein nr. In it, identical
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sequences are merged into one entry. To be merged two sequences must
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have identical lengths and every residue at every position must be the
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same. The FASTA deflines for the different entries that belong to one
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nr record are separated by control-A characters invisible to most
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programs. In the example below both entries gi|1469284 and gi|1477453
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have the same sequence, in every respect:
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>gi|3023276|sp|Q57293|AFUC_ACTPL Ferric transport ATP-binding protein afuC
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^Agi|1469284|gb|AAB05030.1| afuC gene product ^Agi|1477453|gb|AAB17216.1|
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afuC [Actinobacillus pleuropneumoniae]
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MNNDFLVLKNITKSFGKATVIDNLDLVIKRGTMVTLLGPSGCGKTTVLRLVAGLENPTSGQIFIDGEDVT
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KSSIQNRDICIVFQSYALFPHMSIGDNVGYGLRMQGVSNEERKQRVKEALELVDLAGFADRFVDQISGGQ
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QQRVALARALVLKPKVLILDEPLSNLDANLRRSMREKIRELQQRLGITSLYVTHDQTEAFAVSDEVIVMN
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KGTIMQKARQKIFIYDRILYSLRNFMGESTICDGNLNQGTVSIGDYRFPLHNAADFSVADGACLVGVRPE
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AIRLTATGETSQRCQIKSAVYMGNHWEIVANWNGKDVLINANPDQFDPDATKAFIHFTEQGIFLLNKE
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The syntax of sequence header lines used by the NCBI BLAST server
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depends on the database from which each sequence was obtained. The table
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below lists the identifiers for the databases from which the sequences
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Database Name Identifier Syntax
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============================ ========================
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GenBank gb|accession|locus
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EMBL Data Library emb|accession|locus
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DDBJ, DNA Database of Japan dbj|accession|locus
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Protein Research Foundation prf||name
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SWISS-PROT sp|accession|entry name
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Brookhaven Protein Data Bank pdb|entry|chain
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Patents pat|country|number
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GenInfo Backbone Id bbs|number
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General database identifier gnl|database|identifier
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NCBI Reference Sequence ref|accession|locus
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Local Sequence identifier lcl|identifier
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"gi" identifiers are being assigned by NCBI for all sequences contained
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within NCBI's sequence databases. The "gi" identifier provides a uniform
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and stable naming convention whereby a specific sequence is assigned its
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unique gi identifier. If a nucleotide or protein sequence changes,
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however, a new gi identifier is assigned, even if the accession number
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of the record remains unchanged. Thus gi identifiers provide a mechanism
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for identifying the exact sequence that was used or retrieved in a given
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We recommend that "gi display option" be activated in local blast search
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by setting the -I option to T, which was set to false by default:
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-I Show GI's in deflines [T/F]
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For databases whose entries are not from official NCBI sequence databases,
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such as Trace database, the gnl| convention is used. For custom database,
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this convention should be followed and the id for each sequence must be
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unique, if one would like to take the advantage of indexed database,
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which enables specific sequence retrieval using fastacmd program included
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in the blast executable package. One should refer to documents
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distributed in the standalone BLAST package for more details.
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6. Formatting the FASTA database
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FASTA database files need to be formatted with formatdb before they can be
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used in local blast search. For those from NCBI, the following formatdb
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formatdb �i input_db �p F �o T for nucleotide
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formatdb �i input_db �p T �o T for protein
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The -A option introduced in 2.2.3 is now built into the formatdb program
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and thus removed from the list of configurable options since 2.2.8. This
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enables formatdb to properly handle large sequence files (longer than 16
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million bases). Please refer to formatdb.txt under the /blast/documents
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directory for more information. Database preprared using 2.2.8 formatdb
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will not be backward compatible with blast programs old than version 2.2.3.
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Questions and comments on this document and NCBI BLAST related questions
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should be sent to blast-help group at:
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blast-help@ncbi.nlm.nih.gov
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For information about other NCBI resources/services, please send email to
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NCBI User Serivce at:
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info@ncbi.nlm.nih.gov
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doc/blastdb.txt
