Web-based NCBI Blast+ for Windows

Even though command-line NCBI BLAST+ is available for Windows, web-based interface like wwwblast for NCBI BLAST+ is not available and we had to enter long and tedious options to perform BLAST searches on Windows until now. 
Here is a web-based interface for NCBI BLAST+ for Windows. This software was originally developed by NCBI for cloud Linux servers and we ported it to Windows. Procedure below is confirmed to work fine on 64-bit Windows 7 and Windows 10

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.


  • 64-bit Windows 7 or Windows 10


 Install XAMPP package

Launch your browser, type in address bar, and hit enter. If you DO NOT see "This site can't be reached" or "This page can’t be displayed" page, some software is using the default www port 80 and XAMPP won't work. In that case, contact us for paid support.
  • Visit XAMPP site
  • Download XAMPP for Windows. Current version is 5.6.30.
  • Double-click downloaded installer
  • Follow the instructions of installer
  • Select Apache and PHP only in Select Components Window and do not launch XAMPP Control Panel.

 Install strawberry perl

  • Visit strawberry perl site
  • Download 64-bit MSI edition. Current version is
  • Double-click downloaded installer
  • Follow the instructions of installer
  • When the installation is completed, open command prompt and execute the following commands line by line to add necessary modules.
  • cpanm CGI::Application
    cpanm HTML::Table
    cpanm --force Log::Log4perl
    cpanm Carp::Assert
    cpanm Data::Uniqid
    cpanm Number::Bytes::Human

 Install web software

NCBI BLAST+ 2.6.0 is included in the package.
  • Download webblastwin.zip
  • Extract webblastwin.zip. There are blast, cgi-bin, and htdocs folders.
  • Copy blast folder to C:\
  • Copy everything in cgi-bin folder to C:\xampp\cgi-bin
  • Copy everything in htdocs folder to C:\xampp\htdocs

 Launch Server Software

If you want to automatically start servers, put shotcut file of the batch file in Startup folder.
  • Launch Windows File Explorer and go to C:\blast\bin
  • Double-click webblast_start.bat

 Add BLAST databases

  • Create your BLAST database using makeblastdb. Instruction is here.
  • Copy all database files to C:\blast\blastdb_custom.

 How to use

 Access web blast+

  • Launch your favorite browser such as Chrome or Firefox.
  • Type in address bar and hit enter.

 Submit Blast+ job

  • Copy and paste your query sequences into Query field.
  • Select Database you want to use.
  • Select Program you want to use.
  • Select Optional Parameters you want to use.
  • Click BLAST button.

 Blast+ job in Progress

  • In progress page will be shown.

 View Blast+ Results

  • Click Reuqest ID.
  • Blast+ Results will be shown.

 Blast+ Jobs Maintenance

  • Click Recent Results Menu on the top.
  • Click RID to view result.
  • Click red X in Delete results column to delete job.