How To Install and Use NCBI Blast+ on Mac

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.

Procedure below is confirmed to work fine on OS X 10.9 Mavericks, 10.10 Yosemite, and 10.11 El Capitan.   NCBI Blast+ works even on MacBook.
It is assumed that Firefox web browser is installed on your Mac and set as a default browser.  If you do not have Firefox, you can download it from here for free.  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. 

NCBI Blast+ version here is 2.4.0 released on 6/1/2016. If you prefer newer version of NCBI Blast+, try web-based NCBI Blast+. It support NCBI Blast+ 2.6.0.

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

  • Click the link to download installer from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.4.0/ncbi-blast-2.4.0+.dmg
  • Check "Open with DiskImageMounter(Default)" and Click OK
  • Double click ncbi-blast-2.4.0+.pkg. If you see the dialog below, Hold down the Control key and click ncbi-blast-2.4.0+.pkg. From the contextual menu choose Open.
  • Follow the instructions of installer
    All program will be installed under "/usr/local/ncbi/blast/bin”
    If you want to uninstall, double click uninstall_ncbi_blast.zip in mounted disk image to extract it and launch it.
        README.txt which contains the link to he BLAST Help web page will be installed in "/usr/local/ncbi/blast/doc”.             user_manual.pdf is not bundled with the installer anymore.

2. Setup environments

  • In order to use NCBI Blast+, Blast database file location should be specfied. One option is .ncbirc file.
  • Make .ncbirc text file in your home folder. One example is shown below.  Your account is assumed to be MyAccount.
; Start the section for BLAST configuration
[BLAST]
; Specifies the path where BLAST databases are installed
BLASTDB=/Users/MyAccount/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=/Users/MyAccount/blast/db/windowmasker
; end of file
  • Create BLAST database directory.
    1) Open Applications/Utilities/Terminal.
    2) Type "mkdir -p ~/blast/db" and type return.
  • Installer will install /etc/paths.d/ncbi_blast to set path.

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 ~/blast/db
  • Open Applications/Utilities/Terminal.
  • Type "cd ~/blast/db" and type return.
  • Type "tar xfz nt.00.tar.gz" and type return.  nt.00.tar.gz should be the file name you downloaded.  Downloaded file will be extracted in ~/blast/db.

4. Create database

  • Download or create FASTA file.  File name is assumed to be testdb.fasta.
  • Copy testdb.fasta to ~/blast/db.
  • Open Applications/Utilities/Terminal.
  • Type "cd ~/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 Applications/Utilities/Terminal.
    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 Applications/Utilities/Terminal.
    2) Type "blastp -query test_protein.fasta -db nr.00 -out test.html -html" and type return.
    3) Type "blastn -help" for advanced options.
  • How to use multi cores for Blast search
    1) Add "-num_threads 2" to use 2 cores.
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