BlastStation: How To Install and Use NCBI Blast+ on Windows

How To Install and Use NCBI Blast+ on Windows

This page is prepared for the people who want to use NCBI Blast+ on local machines, because we found most of the NCBI Blast+ information available on the Internet is out-dated or inaccurate.
You can find a review for several installation instructions available on the Internet here. You will be surprised with the results.
This instruction supports newest version of NCBI Blast+ (ver. 2.7.1) released on 10/18/2017.
If you don't like to type blast commands, try web-based NCBI Blast+.

Procedure below is confirmed to work fine on Windows 10 This instruction does not cover all blast derivatives, such as blastx, mega blast or psiblast. If you want to use these blast programs, please refer to http://www.ncbi.nlm.nih.gov/books/NBK1763/. We hope information there is correct.

If you don't understand any part of the instruction below, we recommend you to try BlastStation2 or BlastStation-Local64 to save time. You can start Blast search in less than five minutes with the intuitive manner of operation, amazing easy-to-use interface, and useful extra functions including summary table exporting in CSV format and hit sequence exporting in FASTA format.

1. Installation

32-bit Windows

NCBI Blast+ 2.3.0 or later does not support 32-bit Windows. Even though 64-bit NCBI Blast+ will not start on 32-bit Windows, it can be installed on 32-bit Windows because of the lack of the OS version check function.

Click the link to download installer from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-win32.exe
Double click ncbi-blast-2.2.30+-win32.exe to launch installer
Follow the instructions of installer
All program will be installed under "C:Program Files\NCBI\blast-2.2.30+\bin"
README.txt which contains the link to he BLAST Help web page will be installed in "C:Program Files\NCBI\blast-2.2.30+\doc". user_manual.pdf is not bundled with the installer anymore.
Uninstaller is found in "C:Program Files\NCBI\blast-2.2.30+".

64-bit Windows

Click the link to download installer from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe
Double click ncbi-blast-2.7.1+-win64.exe to launch installer
Follow the instructions of installer
All program will be installed under "C:Program Files\NCBI\blast-2.7.1+\bin"
README.txt which contains the link to he BLAST Help web page will be installed in "C:Program Files\NCBI\blast-2.7.1+\doc". user_manual.pdf is not bundled with the installer anymore.
Uninstaller is found in "C:Program Files\NCBI\blast-2.7.1+".

2. Setup environments

In order to use NCBI Blast+, Blast database file location should be specfied. One option is ncbi.ini file.
Make ncbi.ini text file in C:\Windows directory. One example is shown below. Since \ should be escaped with \ in this file, there are two \s instead of one.

; Start the section for BLAST configuration
[BLAST]
; Specifies the path where BLAST databases are installed
BLASTDB=C:\\blast\\db
; Specifies the data sources to use for automatic resolution
; for sequence identifiers
DATA_LOADERS=none
; Specifies the BLAST database to use resolve protein sequences
;BLASTDB_PROT_DATA_LOADER=nr
; Specifies the BLAST database to use resolve protein sequences
;BLASTDB_NUCL_DATA_LOADER=nt
; Windowmasker settings (experimental)
[WINDOW_MASKER]
WINDOW_MASKER_PATH=C:\\blast\\db\\windowmasker
; end of file

Create BLAST database directory.
1) Open command prompt. If you don't know how to do this, visit http://www.howtogeek.com/235101/10-ways-to-open-the-command-prompt-in-windows-10/
2) Type "cd C:\”
3) Type "mkdir blast\db" and type return.

3. Download database

Click the link to visit NCBI ftp server. ftp://ftp.ncbi.nih.gov/blast/db/
Double click the database file you want to download, such as nt.00.tar.gz.
Save the file in C:\blast\db.
Extract downloaded tar.gz file. If you don't have such a software, 7-zip is convenient.

4. Create database

Download or create FASTA file. File name is assumed to be testdb.fasta.
Copy testdb.fasta to C:\blast\db directory using Windows Explorer.
Open command prompt. If you don't know how to do this, visit http://www.sevenforums.com/tutorials/947-command-prompt.html (Windows 7) or http://www.intowindows.com/how-to-open-command-prompt-as-administrator-in-windows-8-1/ (Windows 8.1) or http://www.howtogeek.com/235101/10-ways-to-open-the-command-prompt-in-windows-10/ (Windows 10)
Type "cd C:\blast\db" and type return.
Type "makeblastdb -in testdb.fasta -out testdb -dbtype nucl" for DNA or "makeblastdb -in testdb.fasta -out testdb -dbtype prot" for Protein and type return to get the database named testdb.
Type "makeblastdb -help" for advanced options.

5. Launch NCBI-Blast+ commands

Create dna or protein query FASTA file. It can contain multi FASTA data. File name is assumed to be test_dna.fasta and test_protein.fasta here. nt.00 is a dna database file and nr.00 is a protein database file available at ftp://ftp.ncbi.nih.gov/blast/db/. These database files are assumed to be downloaded already.
blastn
1) Open command prompt.
2) Type "blastn -query test_dna.fasta -db nt.00 -out test.html -html" and type return.
3) Type "blastn -help" for advanced options.
blastp
1) Open command prompt.
2) Type "blastp -query test_protein.fasta -db nr.00 -out test.html -html" and type return.
3) Type "blastn -help" for advanced options.