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!

Overview

• GASSST finds global alignments of short DNA sequences against large DNA banks.

• GASSST strong point is its ability to perform fast gapped alignments.

• It works well for both short and longer reads. It currently has been tested for reads up to 500bp.

• The software is freely available for download under the CECILL version 2 License.

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 :

• bank_file : a collection of DNA sequences of any length (from short EST sequence to full genome).

• query file : a collection of very short DNA sequences.

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

Download

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

• Source Gassst v 1.28 : [tar.gz]

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):

• A few bugs were fixed (particularly in gassst_to_sam.cpp).

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

• Fixed bug and memory leaks for very large reads.

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

• gassst to sam now output results in the same ordre as the query file

• option -g now specifies maximum number of gaps by percentage of the query length.

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

• Added option in gassst_to_sam to output multiple results per read in the sam format, not only the best one.

• Support for even larger reads.

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

• bug in sam format generation causing read sequences to be sometimes erroneously reversed when it should not and vice-versa.

• fixed crashes for extra long ( > 1000 nt ) reads.

New in version 1.24 :

• added support for processors without ssse3 (-amd flag at compilation)

New in version 1.23 :

• added tool to convert to sam format.

• Automatic seed length calculation.

Authors

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

Current and former development contributors

• Dominique Lavenier (lavenier@irisa.fr)

• Guillaume Rizk (grizk@irisa.fr)

• Damien Fleury