ssahaEST: Sequence Search and Alignment by Hashing Algorithm 

ssahaEST is a software tool for very fast matching and alignment of ESTs/cDNAs to genomic DNA sequences.

Archive Page

This page is maintained as a historical record and is no longer being updated.

Archive Page – this page is maintained as a historical archive and is no longer being updated.


It uses the same core algorithms as ssaha2 for sequence matching and contains implementation of Smith-Waterman sequence alignment code from cross_match developed by Phil Green at the University of Washington. Hits produced by the alignment algorithm are clustered into potential transcripts and coordinates of exons are adjusted using several splice site models to produce spliced alignments.

Further information

Contact the authors for further information.

Copyright (C) 2004 – 2006 Genome Research Ltd.

Authors: Nikolai Ivanov, Adam Spargo and Zemin Ning SSAHA2 is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see


If you need help or have any queries, please contact us using the details below.

Contact Zemin Ning for more information.

Sanger Institute Contributors

Photo of Dr Zemin Ning

Dr Zemin Ning

Senior Scientific Manager

External Contributors

Photo of Dr Nikolai Ivanov

Dr Nikolai Ivanov