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MassBlast was developed by André Veríssimo and Jean-Etienne Brassard and is released under GNU General Public License version 3

Download links


BLAST+ (see table in Install section)


Command line application to perform BLAST queries from multiple files against different databases at once.

A pre-print of the manuscript describing this application is available at bioRxiv and can be accessed here.

General description of the MassBlast workflow:

Pipeline of MassBlast


  1. Download BLAST+ and MassBlast from the links in the table below
  2. BLAST+ must be installed and available from a command line
    • check by running the command: blastn -version
  3. Decompress MassBlast and it is ready to be used using the mass-blast script
MassBlast downloads Windows Mac OS X Linux
BLAST+ (pre-requirement) v2.2.30 (32-bit) v2.6.0 2.6.0

BLAST+ important notes

  1. Must be installed before MassBlast is run
  2. Windows users
    1. Must install 32-bit version v2.2.30 of BLAST+
    2. In case of an error in the first run:
      • Delete ncbi.ini located at a subdirectory at the AppData folder in the user directory
      • If problem persists, submit an issue.
  3. Mac OS X and Linux users
    • MassBlast was tested with version 2.6.0, but it could work with more recent versions (or older and down to v2.2.30)

note: Ruby and all other requirements are included in the package files, it is not necessary to install when using packaged version.

How to use MassBlast?

Example of a nucleic-acid query file that could be placed in db_and_queries/queries folder:


Type of BLAST methods available

The method is defined in the file user.yml

How to setup a Blast database for a transcriptome

Using makeblastdb command that comes bundled with Blast+

note: do to not use spaces in the <blast db new name>

Quickly setup databases

Place the fasta files for the database in db_and_queries/import_dbs directory and run the appropriate script.

You also need to say if it is a nucleic-acid or protein-based fasta file.

For Linux and Mac OS X run the script

$ cd db_and_queries/import_dbs
# for nucleic-acid
$ sh nucl
# for protein
$ sh prot

For Windows run the import_fastas.bat script

$ cd db_and_queries/import_dbs
# for nucleic-acid
$ import_fastas.bat nucl
# for protein
$ import_fastas.bat prot


MassBlast was developed primarily by André Veríssimo, Jean-Etienne Bassard and Susana Vinga

A pre-print of the manuscript is available at bioRxiv and can be accessed here

This work was supported by:

We would like to thank Cathie Martin and Philippe Vain for reading the manuscript and providing us with important comments and insights. We would also like to thank Aldo Ricardo Almeida Robles and Nuno Mira for testing MassBlast.