Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models

@article{Yu2001StatisticalSO,
  title={Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden Markov Models},
  author={Yi-Kuo Yu and Terence Hwa},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2001},
  volume={8 3},
  pages={249-82}
}
The score statistics of probabilistic gapped local alignment of random sequences is investigated both analytically and numerically. The full probabilistic algorithm (e.g., the "local" version of maximum-likelihood or hidden Markov model method) is found to have anomalous statistics. A modified "semi-probabilistic" alignment consisting of a hybrid of Smith-Waterman and probabilistic alignment is then proposed and studied in detail. It is predicted that the score statistics of the hybrid… CONTINUE READING

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