Basic Sequence Search by Hashing Algorithm in DNA Sequence Databases

We designed a new genome search tool, basic sequence search by hashing algorithm (BSSHA) bases on basic local alignment search tool (BLAST) and, sequence search and alignment by hashing algorithm (SSAHA) for DNA sequence databases. Preprocess query sequence by making m-letter word list. Sequences in the database are preprocessed by breaking them into k-tuples of k-contiguous bases and hash table is created to store the position of each occurrence of each k-tuple. "Linked list" method is applied to search a query sequence in the database by detecting the hits in the hash table. Hash table for database is generated only once since it can be saved in the memory for further use. BSSHA depends on exact matching pair, so it enables execution time shorter by skipping those empty hit list or low possibility matches. Time complexity theory shows that the execution time for BSSHA is shorter than SSAHA.