Search and pattern discovery Sequences (DNA, RNA) Structure (RNA, protein)
Functionally significant regions, repeated in different entities, often described by patterns.
Search through (very large) genome / protein databases for entries matching the pattern. ( formal language theory,- [Searles93].
Biological data is noisy: string languages - stochastic approaches
- Hidden Markov models [Durbin et al, 98]
- Stochastic context-free grammars [Lathrop&Smith, 96].