Part I : How to install NCBI BLAST on window 7

Swati Srivastva asked to use
hou to use and install ncbi blast offline cammands
Actually every use of software includes three steps.

  • Download
  • Installation 
  • Uses
In this Part of tutorial, lets discuss two steps of the NCBI blast 
process. blast+ is a new version of the blast package from the NCBI.
The blast+ package consists of a number of stand-alone programs, for searching sequence databases, creating blast databases and masking low complexity sequence.

Benefits of  NCBI blast+ :

  • Easy to local blast searhcers, and easy to run remote searches at the NCBI from the command line. 
  • You can save search strategies and run them again later.
  • Flexible output of blast results. For example, you can get tab delimited output AND choose which columns of information are included.
  • blastx efficiency has apparently been increased.
  • An option to enable multiple threads to be run for local blast searches
  • Blasting 2 sequences against each other is now easier
1. Download
  • Latest executable of NCBI stand alone BLAST can be download from HERE. This directory contains executable for Window, Linux and Mac. Lets go with window executable. You can simply download it your favorite location (desktop, for me). 
  • Double click on downloaded files will resulted in a directory with the three files : Uninstaller, bin and doc folders. All  executable will be in bin folder while all documentation will be in doc folders. 
  • Since all BLAST  executable are non GUI therefore you have to access those  executable through command line option of Window cmd.


2. Uses
bin folder of of NCBI local BLAST programms contains two type of program. remember that you can always use 'program name -help' command to know more about that program. For example, if you want to know abput blastp then use 'blastp -help'.
  • .exe files
  • PERL scripts
.exe files are three used for three different purpose 
  • database searching 
  • creating and working with database 
  • sequence masking utilities
Sequence Masking Utilities
    segmasker used to mask repeats and low-complexity regions in a genome sequence
    dustmasker used to identifies and masks out low complexity parts of a genome using a new and improved DUST algorithm
    windowmasker used to identifies and masks highly repetitive DNA sequences in a genome, using only the sequence of the genome itself.

    Database Searching Utilities

    Explained here
    rpsblast+ searches a query sequence against a database of profiles, or score matrices, prepared by copymat, producing BLAST-like output
    rpstblastn searches database of profiles using a translated nucleotide query against
    deltablast Explained here

    Sequence Masking Utilities

    makeblastdb command-line tool for creating BLAST databases
    makembindex utility that can index a set of nucleotide sequences
    blastdbcmd command-line tool to examine the contents of BLAST databases
    makeprofiledb used to make search sets for RPS-BLAST, including the specialized data needed by DELTA-BLAST
    blastdbcheck performs tests on BLAST databases to check their integrity
    blastdb_aliastool Use to manage the collection of BLAST databases and facilitate BLAST searches.
    blast_formatter formats both local and remote BLAST results
    convert2blastmask extracts the lower-case masks from its FASTA input and converts them to a file format suitable for specifying masking information to makeblastdb

    PERL Script

    legacy_blast Script to convert NCBI C toolkit command line program and arguments into NCBI C++ toolkit command line program and arguments for the BLAST suite of programs
    update_blastdb Script to download the pre-formatted BLAST databases from the NCBI ftp server.

    Further Uses

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