SSAHA
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Application data |
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| Created by | Adam Spargo, Zemin Ning |
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| Principal bioinformatics method(s) | Sequence alignment, Local sequence alignment |
| Technology | Sanger, 454, Illumina |
| Created at | The Wellcome Trust Sanger Institute |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | GFF, SUGAR, CIGAR, VULGAR, PSL, PSLX, SAM |
| Licence | Commercial, Freeware |
| Operating system(s) | Linux, Mac OS X |
| Contact: | jcm@sanger.ac.uk |
Summary: SSAHA (Sequence Search and Alignment by Hashing Algorithm) is an algorithm for very fast matching and alignment of DNA sequences.
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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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