Abstract
An algorithm for computing the probabilities of biological sequences is presented. The algorithm is applicable to many problems of bioinformatics, in particular, computing seed sensitivity in the search for local similarities in genomes or estimating the reliability of search for clusters of regulatory sites. It can be also used for distributions of probabilities described by different models, e.g., Bernoulli, Markov, and hidden Markov models. The algorithm is based on the description of probability distribution as well as of the family of sequences using finite automata, whereby the problem of calculating the probabilities is reduced to computing an appropriate generalized partition function. The algorithm can be applied not only to biological sequences but also to symbol sequences of any origin.
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Abbreviations
- (D)FA:
-
(deterministic) finite automaton
- GPF:
-
generalized partition function
- HMM:
-
hidden Markov models
- PAA:
-
probabilistic accepting automaton
- PT:
-
probability transducer.
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Original Russian Text © M.A. Roytberg, 2009, published in Biofizika, 2009, Vol. 54, No. 5, pp. 791–797.
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Roytberg, M.A. Computation of the probabilities of families of biological sequences. BIOPHYSICS 54, 569–573 (2009). https://doi.org/10.1134/S0006350909050029
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DOI: https://doi.org/10.1134/S0006350909050029