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                         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 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

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 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

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 bi-weekly. 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

$Header: /src/NCBI/vault.ncbi/distrib/doc/blast/blastdb.html,v 1.10 2008/10/02 16:01:03 camacho Exp $
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blast2 1:2.2.25.20110713-3ubuntu2 / usr / share / doc / blast2 / blastdb.html
