String analysis and energy minimization in the partition of DNA sequences.
Two approaches to the understanding of biological sequences are confronted. While the recognition of particular signals in sequences relies on complex physical interactions, the problem is often analysed in terms of the presence or absence of literal motifs (strings) in the sequence. We present here a test-case for evaluating the potential of this approach. We classify DNA sequences as positive or negative depending on whether they contain a single melted domain in the middle of the sequence, which is a global physical property. Two sets of positive "biological" sequences were generated by a computer simulation of evolutionary divergence along the branches of a phylogenetic tree, under the constraint that each intermediate sequence be positive. These two sets and a set of random positive sequences were subjected to pattern analysis. The observed local patterns were used to construct expert systems to discriminate positive from negative sequences. The experts achieved 79% to 90% success on random positive sequences and up to 99% on the biological sets, while making less than 2% errors on negative sequences. Thus, the global constraints imposed on sequences by a physical process may generate local patterns that are sufficient to predict, with a reasonable probability, the behaviour of the sequences. However, rather large sets of biological sequences are required to generate patterns free of illegitimate constraints. Furthermore, depending upon the initial sequence, the sets of sequences generated on a phylogenetic tree may be amenable or refractory to string analysis, while obeying identical physical constraints. Our study clarifies the relationship between experts' errors on positive and negative sequences, and the contributions of legitimate and illegitimate patterns to these errors. The test-case appears suitable both for further investigations of problems in the theory of sequence evolution and for further testing of pattern analysis techniques.
Ninio
J
J
Institut Jacques Monod, Paris, France.
Mizraji
E
E
D001483:Base Sequence; D004247:DNA; D007700:Kinetics; D008957:Models, Genetic; D010802:Phylogeny; D011336:Probability
D004247:DNA