SSAHAest

SSAHAest

SSAHAest

Archive Page - this page is maintained as a historical archive and is no longer being updated.

Overview

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 <http://www.gnu.org/licenses/>.

Contact

Contact Zemin Ning for more information.

Authors

Sanger Contributors
External Contributors

Publications

  • 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