Introduction

NCBI provides command line standalone BLAST+ programs (based on the NCBI C++ toolkit) as a single compressed package. The package is available for the Linux, Mac OSX, and Windows platforms at:

https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/

The archives for Linux and Mac OSX are available as gzip-compressed tar files named using the following convention:

ncbi-blast-#.#.#+-CHIP-OS.tar.gz

Here, the #.#.# represents the version number of the current release, CHIP indicates the chipset, and OS indicates the operating system. Equivalent .rpm and .dmg files for Linux and Mac OSX are also available. These archives and their target platforms are listed in the table below.

The installation process from the disk image (.dmg) for Mac OSX and the Red Hat Package Manger (.rpm) for Linux requires administrative privileges and will not be discussed here. More information is available here: http://www.ncbi.nlm.nih.gov/books/NBK279671/.

Downloading

The BLAST+ packages for various platforms can be downloaded through anonymous ftp using an ftp client, wget, curl, or a web browser. The example working session below demonstrates an ftp download process using an ftp client in a Linux environment. In Mac OSX, a similar command line interface is available through the Terminal utility, which is generally under the Utilities folder.

$ ncftp ftp.ncbi.nlm.nih.gov
NcFTP 3.2.5 (Feb 02, 2011) by Mike Gleason (http://www.NcFTP.com/contact/).
Connecting to ftp.ncbi.nlm.nih.gov...                                                           

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 Unauthorized or improper use of this system is prohibited and may result in 
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FTP Server ready.
Logging in...                                                                                   
Anonymous access granted, restrictions apply
Logged in to ftp.ncbi.nlm.nih.gov.                                                              
ncftp / > cd /blast/executables/LATEST/  << change directory to the LATEST
ncftp /blast/executables/LATEST > bin    << set transfer mode to binary
ncftp /blast/executables/LATEST > get ncbi-blast-2.10.1+-x64-linux.tar.gz
ncbi-blast-2.10.1+-x64-linux.tar.gz:                   224.64 MB   37.27 MB/s  
ncftp /blast/executables/LATEST > bye
$

vog.hin.mln.ibcn@xobloot 

Installation

To install, simply extract the downloaded package after placing it under a desired directory. This can be accomplished by a single tar command, or a combination of gunzip and tar commands.

$ tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz 

or

$ gunzip -d ncbi-blast-2.10.1+-x64-linux.tar.gz
$ tar xvpf ncbi-blast-2.10.1+-x64-linux.tar

Successful execution of the above commands installs the package and generates a new ncbi-blast-2.10.1+ directory under the working directory selected. This new directory contains the bin and doc subdirectories, as well as a set of informational files. The bin subdirectory contains the programs listed below.

Configuration

Using the BLAST+ package installed above without configuration will be cumbersome – it requires the installation path to be prefixed to the program and database calls since the system does not know where to look for the installed program and the specified database. To streamline BLAST searches, two environment variables, PATH and BLASTDB, need to be modified and created, respectively, to point to the corresponding directories.

Under bash, the following command appends the path to the new BLAST bin directory to the existing PATH setting:

                $ export PATH=$PATH:$HOME/ncbi-blast-2.10.1+/bin
              

The equivalent command under csh is:

                $ setenv PATH ${PATH}:/home/tao/ncbi-blast-2.10.1+/bin
              

The modified $PATH can be examined using echo (added portion underlined):

$ echo $PATH
/usr/X11R6/bin:/usr/bin:/bin:/usr/local/bin:/opt/local/bin:/home/tao/ncbi-blast-2.10.1+/bin

To manage available BLAST databases, create a directory to store them:

                $ mkdir $HOME/blastdb
              

Use the approaches described above for PATH to set the BLASTDB value under bash:

                $ export BLASTDB=$HOME/blastdb
              

Or under csh to create it anew:

                $ set BLASTDB=$HOME/blastdb
              

A better approach is to have the system automatically set these variables upon login, by modifying the .bash_profile or .cshrc file.

Once they are set, the system knows where to call BLAST programs, and the invoked program will know where to look for the database files. Note that with BLASTDB unspecified, BLAST+ programs only search the working directory, i.e. the directory where BLAST command is issued. For more details about configuring BLAST+, please see http://www.ncbi.nlm.nih.gov/books/NBK279695/.

Database Download

BLAST database is a key component of any BLAST search. To fully test the BLAST+ package, a functional database is needed. The following working session demonstrates the process of downloading and installing a single-volume database named 16S_ribosomal_RNA from NCBI, using the update_blastdb.pl script included in the /bin directory.

$ cd $HOME/blastdb

$ perl ../bin/update_blastdb.pl --passive --decompress 16S_ribosomal_RNA
Connected to NCBI
Downloading 16S_ribosomal_RNA.tar.gz... [OK]
Decompressing 16S_ribosomal_RNA.tar.gz ... [OK]
$ ls -l 
total 172388
-rw-r--r-- 1 tao sdesk   1142784 Jun  6 12:05 16S_ribosomal_RNA.ndb
-rw-r--r-- 1 tao sdesk   3326945 Jun  6 12:05 16S_ribosomal_RNA.nhr
-rw-r--r-- 1 tao sdesk    252508 Jun  6 12:05 16S_ribosomal_RNA.nin
-rw-r--r-- 1 tao sdesk    170664 Jun  6 12:05 16S_ribosomal_RNA.nnd
-rw-r--r-- 1 tao sdesk       716 Jun  6 12:05 16S_ribosomal_RNA.nni
-rw-r--r-- 1 tao sdesk     84152 Jun  6 12:05 16S_ribosomal_RNA.nog
-rw-r--r-- 1 tao sdesk    424244 Jun  6 12:05 16S_ribosomal_RNA.nos
-rw-r--r-- 1 tao sdesk    252764 Jun  6 12:05 16S_ribosomal_RNA.not
-rw-r--r-- 1 tao sdesk   7761701 Jun  6 12:05 16S_ribosomal_RNA.nsq
-rw-r--r-- 1 tao sdesk    548864 Jun  6 12:05 16S_ribosomal_RNA.ntf
-rw-r--r-- 1 tao sdesk    148812 Jun  6 12:05 16S_ribosomal_RNA.nto
-rw-r--r-- 1 tao sdesk        59 Jun 11 12:14 16S_ribosomal_RNA.tar.gz.md5
-rw-r--r-- 1 tao sdesk 146879591 Jun  6 12:05 taxdb.btd
-rw-r--r-- 1 tao sdesk  15506928 Jun  6 12:05 taxdb.bti
$ 

For databases with multiple volumes, update_blastdb.pl will automatically get all of them. For databases already installed locally, update_blastdb.pl will compare it against that on the NCBI ftp site to determine if refreshing is needed.

$ perl ../bin/update_blastdb.pl --passive --decompress 16S_ribosomal_RNA
Connected to NCBI
The contents of 16S_ribosomal_RNA.tar.gz are up to date in your system.
$ 

Execution and validation

With the above configuration, BLAST programs installed under the "ncbi-blast-2.10.1+/bin" directory can be invoked by name from any directory. Type the command "blastn -help" (without quotes) should display the program parameters of blastn in the console as shown below.

$ blastn -help
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-seqidlist filename]
    [-negative_gilist filename] [-entrez_query entrez_query]
    [-db_soft_mask filtering_algorithm] [-db_hard_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-xdrop_ungap float_value]
    [-xdrop_gap float_value] [-xdrop_gap_final float_value]
    [-searchsp int_value] [-max_hsps int_value] [-sum_statistics]
    [-penalty penalty] [-reward reward] [-no_greedy]
    [-min_raw_gapped_score int_value] [-template_type type]
    [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]
    [-window_masker_taxid window_masker_taxid]
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-window_size int_value]
    [-off_diagonal_range int_value] [-use_index boolean] [-index_name string]
    [-lcase_masking] [-query_loc range] [-strand strand] [-parse_deflines]
    [-outfmt format] [-show_gis] [-num_descriptions int_value]
    [-num_alignments int_value] [-html] [-max_target_seqs num_sequences]
    [-num_threads int_value] [-remote] [-version]

DESCRIPTION
   Nucleotide-Nucleotide BLAST 2.2.29+

OPTIONAL ARGUMENTS
 -h
   Print USAGE and DESCRIPTION;  ignore all other parameters
 -help
   Print USAGE, DESCRIPTION and ARGUMENTS; ignore all other parameters
 -version
   Print version number;  ignore other arguments

 *** Input query options
 -query <File_In>
   Input file name
   Default = `-'
 -query_loc <String>
   Location on the query sequence in 1-based offsets (Format: start-stop)
 -strand <String, `both', `minus', `plus'>
   Query strand(s) to search against database/subject
   Default = `both'
... 
 

For installation without $PATH modification, prefix the path to the program. For example, to execute the same command from /home/tao directory, use the following command instead, where the "./" prefix denotes the current working directory:

/home/tao $ ./ncbi-blast-2.10.1+/bin/blastn –help

                  $ blastdbcmd -db 16S_ribosomal_RNA -entry nr_025000 -out 16S_query.fa
                  

                  

                  $ blastn -db 16S_ribosomal_RNA -query 16S_query.fa -task blastn -dust no -outfmt "7 delim=, qacc sacc evalue bitscore qcovus pident" -max_target_seqs 5
                  

                  

                  # BLASTN 2.10.1+
                  

                  # Query: NR_025000.1 Mycobacterium kubicae strain CDC 941078 16S ribosomal RNA, partial sequence
                  

                  # Database: 16S_ribosomal_RNA
                  

                  # Fields: query acc., subject acc., evalue, bit score, % query coverage per uniq subject, % identity
                  

                  # 5 hits found
                  

                  NR_025000.1,NR_025000,0.0,2383,100,100.000
                  

                  NR_025000.1,NR_028940,0.0,2334,100,99.243
                  

                  NR_025000.1,NR_125568,0.0,2320,100,98.940
                  

                  NR_025000.1,NR_118110,0.0,2302,100,98.637
                  

                  NR_025000.1,NR_117220,0.0,2302,100,98.637
                  

                  # BLAST processed 1 queries
                  

                  

                  $
                

Technical Assistance

Questions, feedback, and technical assistance requests should be sent to blast-help at:

vog.hin.mln.ibcn@pleh-tsalb 

Questions on other NCBI resources should be addressed to NCBI User Services at:

vog.hin.mln.ibcn@ofni