Inductive Inference over Macro-Molecules

Minimum message length techniques are applied to problems over strings such as biological macro-molecules. This allows the posterior odds-ratio of two theories or hypotheses about strings to be calculated. Given two strings we compare the r-theory, that they are related, with the null-theory, that they are not related. This is done for one, three and five-state models of relation. Models themselves can be compared and this is done on real DNA strings and artificial data. A fast, approximate MML string comparison algorithm is also described.