A generalized method for matching informational macromolecular code sequences

Wong, Andrew K. C.; Reichert, Tom; Cohen, Danny; Aygun, Betul

doi:10.1016/0010-4825(74)90006-7

Cited by 19 publications

(3 citation statements)

References 8 publications

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“…The MML method does not suffer from this problem and has a formal interpretation of differences in message length and indeed has a rigorous test of statistical significance. Reichert et al (1973), Wong et al (1974), and Cohen et al (1975) first considered the brief encoding of pairs of strings under a nonstandard model of relation but did not compare models. Milosavljevic (1990) considered the classification of aligned macromolecules by MML methods.…”

Section: P(handd) = P(d [ H) P(h) = P(h [ D)p(d)mentioning

confidence: 99%

Finite-state models in the alignment of macromolecules

1992

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Minimum message length encoding is a technique of inductive inference with theoretical and practical advantages. It allows the posterior odds-ratio of two theories or hypotheses to be calculated. Here it is applied to problems of aligning or relating two strings, in particular two biological macromolecules. We compare the r-theory, that the strings are related, with the null-theory, that they are not related. If they are related, the probabilities of the various alignments can be calculated. This is done for one-, three-, and five-state models of relation or mutation. These correspond to linear and piecewise linear cost functions on runs of insertions and deletions. We describe how to estimate parameters of a model. The validity of a model is itself an hypothesis and can be objectively tested. This is done on real DNA strings and on artificial data. The tests on artificial data indicate limits on what can be inferred in various situations. The tests on real DNA support either the three- or five-state models over the one-state model. Finally, a fast, approximate minimum message length string comparison algorithm is described.

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Section: P(handd) = P(d [ H) P(h) = P(h [ D)p(d)mentioning

confidence: 99%

Finite-state models in the alignment of macromolecules

1992

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“…Thus, for instance, Fitch [29] utilized the minimal number of genetic mutations that are necessary in getting from one protein to another within a given functional family. Following his work, several other criteria have been implemented [30][31][32] and attempts have been undertaken [33,34] at developing procedures that select correspondencies that satisfy some optimality measure with respect to suitable information-theoretic-like scoring schemes.…”

Section: Similarity and Molecular Taxonomymentioning

confidence: 99%

On the Role of Information and Hierarchy in the Modeling of Biomolecular Systems

Apostolico

1978

Journal of Cybernetics

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“…In the last year, we have developed a measure of the amount of information required to perform genetic mutations, together with an algorithm utilizing these measures, for aligning amino acid and RNA code sequences [9], [11]. In the process of this development, we attempted to calculate the amount of information which was stored in a protein's amino acid sequence.…”

Section: Introductionmentioning

confidence: 99%

The Amount of Information Stored in Proteins and Other Short Biological Code Sequences

Reichert¹

1972

Darwinian, Neo-Darwinian, and Non-Darwinian Evolution, April 9–12, 1971

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A generalized method for matching informational macromolecular code sequences

Cited by 19 publications

References 8 publications

Finite-state models in the alignment of macromolecules

Finite-state models in the alignment of macromolecules

On the Role of Information and Hierarchy in the Modeling of Biomolecular Systems

The Amount of Information Stored in Proteins and Other Short Biological Code Sequences

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