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Computational Systems Bioinformatics
In recent years, sequence database searching has been conducted through local alignment heuristics, patternmatching, and comparison of short statistically significant patterns. While these approaches have unlocked many clues as to sequence relationships, they are limited in that they do not provide context-sensitive searching capabilities (e.g. considering pseudoknots, protein binding positions, and complementary base pairs). Stochastic grammars (hidden Markov models HMMs and stochasticdoi:10.1142/9781860948732_0024 fatcat:hofksr4bavcqfjagm3xeu2qkiy