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.

[Genome Research Limited]


For an academic licence please send us an email to We will provide limited support for academic users, please try to provide enough information for us to recreate any problems you may have. We would be happy to consider any suggestions for new features. If you require binaries for another platform, we will build them if we have one. If you use ssahaEST to accomplish any scientific work please cite this web page.

Usage instructions are obatained from the binary with a '-h' option.

FTP download


* quick link -