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Short description:
Please summarise the application in a few sentences. Avoid links here. SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence alignment, Local sequence alignment,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
Sanger, 454, Illumina,
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
The Wellcome Trust Sanger Institute,
SSAHA achieves its fast search speed by encoding sequence information in a perfect hash function. The SSAHA2 package combines the SSAHA searching algorithm with the cross_match sequence alignment program developed by Phil Green at the University of Washington. The SSAHA algorithm is used to identify regions of high similarity which are then aligned using a banded Local sequence alignment algorithm.
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