3.1: What Have We Learned?
- Page ID
- 40920
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In this section we explored alignment algorithms beyond global alignment. We began by reviewing our use of dynamic programming to solve global alignment problems using the Needleman-Wunsch algorithm. We then the explored alternatives of local (Smith-Waterman) and semi-global alignments. We then discussed using hash function to match exact strings in linear time (Karp-Rabin) as well as doing a neighborhood search, investigating similar sequences in probabilistic linear time (pigeonhole principle, combs, 2-hit blast, random projections). We have also addressed using pre-processing for linear time string matching, as well as the probabilistic background for sequence alignment.