Archive Page: SSAHAest

Archive Page: SSAHAest


Archive Page - this page is maintained as a historical archive and is no longer being updated.


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.

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.

Learn and Support

Contact the authors for further information.

License and Citation

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 <>.


Contact Zemin Ning for more information.


Sanger Contributors
External Contributors


  • SSAHA: a fast search method for large DNA databases.

    Ning Z, Cox AJ and Mullikin JC

    Genome research 2001;11;10;1725-9

Tool Type