SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. Sequences in the database are preprocessed by breaking them into consecutive k-tuples ofk contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple. Searching for a query sequence in the database is done by obtaining from the hash table the “hits” for each k-tuple in the query sequence and then performing a sort on the results. We discuss the effect of the tuple length k on the search speed, memory usage, and sensitivity of the algorithm and present the results of computational experiments which show that SSAHA can be three to four orders of magnitude faster than BLAST or FASTA, while requiring less memory than suffix tree methods. The SSAHAalgorithm is used for high-throughput single nucleotide polymorphism (SNP) detection and very large scale sequence assembly.
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Ning Z, Cox AJ and Mullikin JC
SSAHA: a fast search method for large DNA databases.
Genome research 2001;11;10;1725-9