Continuity in evolution: On the nature of transitions

Science

Volumn 280, Issue 5368, 1998, Pages 1451-1455

  Fontana, Walter ^a   Schuster, Peter ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL POPULATION; EVOLUTION; PHENOTYPE; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; RNA SEQUENCE; SEQUENCE HOMOLOGY;

BASE SEQUENCE; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENOTYPE; MUTATION; NUCLEIC ACID CONFORMATION; PHENOTYPE; RNA; RNA, TRANSFER; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 0032577365     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.280.5368.1451     Document Type: Article

References (39)

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4. Let i, j, k, and I denote positions of bases in the linear sequence and (i, j) denote a base pair. The secondary structure of an RNA sequence is defined as the set P of allowed base pairs (here Watson-Crick pairs plus GU) that minimize free energy, subject to a no-knot condition requiring that if (i, J) and (k, l) are both in P, then i < k < j implies i < l < j (that is, base pairs do not cross). The secondary structure is computed with our implementation (10) of a dynamic programming algorithm, originally from (21), which is widely used in laboratories to assist in the prediction of secondary structures. The procedure is based on empirical energy parameters (22).
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13. The same phenomenon has been observed in optimization problems of a quite different nature, such as the evolution of particle-based computation in cellular automata with the use of genetic algorithms (23).
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15. In RNA folding, some shapes are realized much more frequently than others (11, 25). They were termed common shapes (26), and our statements, based on statistics, can be expected to hold only for these common shapes.
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39. Financial support was provided by the Austrian Fonds zur Förderung der wissenschaftlichen Forschung (Projects P-10578 and P-11065), by HASA Laxenburg, Austria, by the Commission of the European Union (Contract Study PSS*0884), and by the integrative core research at the Santa Fe Institute.