GASSST : Global Alignment Short Sequence Search Tool

GASSST is a free software distributed under the terms of the

CECILL version 2 License

GASSST article is now available!


Usage example :

For alignments with 90 % similarity minimum

Gassst -d bank.fasta -i query.fasta -o results -p 90

Then call "gassst_to_sam" if you want to convert output to SAM format :

./gassst_to_sam results results.sam

The program takes as inputs 2 banks in FASTA format :

For the complete list of options, see the readme file.


GASSST is distributed as source code(C++) under the terms of CECILL version 2 License.

This software was developed using version 4.1.2 of the GNU gcc compiler on a Linux Fedora 8 distribution.

New in version 1.28 (01/08/11):

New in version 1.27 (03/09/11):

New in version 1.266 (03/04/11):

New in version 1.265 (02/16/11):

Bugs corrected in version 1.262 (10/21/10):

New in version 1.24 :

New in version 1.23 :


GASSST is developed whithin the bioinformatics Symbiose group at IRISA-INRIA, Rennes, France.

Current and former development contributors