blast 数据库说明

   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

转载于:https://www.cnblogs.com/xiaofeiIDO/p/6429497.html