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                         The BLAST Databases

                    Last updated on March 1, 2011

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 本地BLAST数据库下载地址

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.这些数据库是已经预先进行过makeblastdb命令的，下载后可以直接使用

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; 可以从这些数据库文件中导出FASTA文件

    * A convenient script (update_blastdb.pl) is available to download 

      the pre-formatted databases from the NCBI ftp site; 可用该脚本升级数据库

    * Pre-formatting removes the need to run formatdb; 无需再运行建库命令行

    * 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). 下载数据库时，需要用到perl脚本update_blastdb.pl，或使用FTP下载工具

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.下载的数据库为压缩包，要解压缩

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). 大的数据库通常分为多个压缩包，例如nr库有11个压缩包。所有的相关压缩包

都要下载，解压。解压缩会生成对应的库文件，同时生成一个nr.pal文件。检索nr库时输入-d nr 即可。

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. 有些数据库是大数据库

的子集，使用这些子集数据库时，必须同时下载其（相同日期的）大数据库

Additional BLAST databases that are not provided in pre-formatted 

formats are available in the FASTA subdirectory. 有些BLAST数据库没有提供预先建库

的文件，这些数据库可以从FASTA文件夹里下载 For genomic BLAST 

databases, please check the genomes ftp directory at:

    ftp://ftp.ncbi.nih.gov/genomes/ 在这里下载基因组BLAST数据库

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.

  数据库名称                 数据库内容

+----------------------+-----------------------------------------------+

|File Name             | Content Description                           |

+----------------------+-----------------------------------------------+

/FASTA                 | subdirectory for FASTA formatted sequences

                         存放FASTA格式序列的子文件夹

    

README                 | README for this subdirectory (this file)

env_nr.*tar.gz         | Environmental protein sequences 环境蛋白序列

env_nt.*tar.gz         | Environmental nucleotide sequences 环境核苷酸序列

est.*tar.gz            | volumes of the formatted est database

                       | from the EST division of GenBank, EMBL, 

                       | and DDBJ.  EST数据库

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. 三类EST数据库子集

gss.*tar.gz            | volumes of the formatted gss database

                       | from the GSS division of GenBank, EMBL, and

                       | DDBJ.  GSS数据库

htgs.*tar.gz           | volumes of htgs database with entries

                       | from HTG division of GenBank, EMBL, and DDBJ.

                         htgs数据库

human_genomic.*tar.gz  | human RefSeq (NC_######) chromosome records

                       | with gap adjusted concatenated NT_ contigs

                         人类染色体的RefSeq参考序列

 

nr.*tar.gz             | non-redundant protein sequence database with 

                       | entries from GenPept, Swissprot, PIR, PDF, PDB,

                       | and NCBI RefSeq 非冗余的蛋白数据库 nr

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. 

                         核苷酸数据库 nt

other_genomic.*tar.gz  | RefSeq chromosome records (NC_######) for 

                       | organisms other than human

                         人类以外的其他生物染色体的RefSeq参考序列

pataa.*tar.gz          | patent protein sequence database 专利蛋白数据库

patnt.*tar.gz          | patent nucleotide sequence database 专利核苷酸数据库

                       | 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. 源于pdb蛋白结构数据库的

                         蛋白序列，其根数据库为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.源于pdb核苷酸结构数据库

                         的核苷酸序列，其根数据库为nt

refseq_genomic.*tar.gz | NCBI genomic reference sequences NCBI基因组参考序列

refseq_protein.*tar.gz | NCBI protein reference sequences NCBI蛋白参考序列

refseq_rna.*tar.gz     | NCBI Transcript reference sequences NCBI转录本参考序列

sts.*tar.gz            | Sequences from the STS division of GenBank, EMBL,

                       | and DDBJ. STS数据库

swissprot.tar.gz       | swiss-prot sequence databases (last major update),

                       | its parent database is nr. weiss-prot蛋白数据库子集，

                         其根数据库为nr

taxdb.tar.gz           | Additional taxonomy information for the formatted 

                       | database (contains common and scientific names)

                         分类学信息

wgs.*tar.gz            | volumes for whole genome shotgun sequence assemblies 

                       | for different organisms. wgs数据库

                

+----------------------+-----------------------------------------------+

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. 使用前需要运行makeblastdb命令行

  文件名                    文件内容

+-----------------------+-----------------------------------------------+

|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 daily.数据库每天升级  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 

at http://www.ncbi.nlm.nih.gov/books/NBK7183/table/ch_demo.T5/?report=objectonly 

lists the supported FASTA identifiers.

"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