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  • 1
    Electronic Resource
    Electronic Resource
    RNA multi-structure landscapes (1993)
    Springer
    European biophysics journal 22 (1993), S. 13-24 
    Details
    ISSN: 1432-1017
    Keywords: Fitness landscapes ; Partition function ; Quasispecies ; RNA secondary structures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest, in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced and pair correlations at the level of the structures themselves are computed. Just as with landscapes based on most stable secondary structure prediction, the landscapes defined on the full biophysical GCAU alphabet are much smoother than the landscapes restricted to pure GC sequences and the correlation lengths are almost constant fractions of the chain lengths. Correlation functions for multi-structure landscapes exhibit an increased correlation length, especially near the melting temperature. However, the main effect on evolution is rather an effective increase in sampling for finite populations where each sequence explores multiple structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00205808
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Dynamical systems under constant organization I. Topological analysis of a family of non-linear differential equations —A model for catalytic hypercycles (1978)
    Springer
    Bulletin of mathematical biology 40 (1978), S. 743-769 
    Details
    ISSN: 1522-9602
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract The paper presents a qualitative analysis of the following systems ofn differential equations: $$\dot x_i = x_i x_j - x_i \sum\nolimits_r^n { = 1} x_r x_s {\mathbf{ }}(j = i - 1 + n\delta _{i1} {\mathbf{ }}and{\mathbf{ }}s = r - 1 + n\delta _{r1} )$$ , which show cyclic symmetry. These dynamical systems are of particular interest in the theory of selforganization and biological evolution as well as for application to other fields.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02460605
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  • 3
    Electronic Resource
    Electronic Resource
    Fast folding and comparison of RNA secondary structures (1994)
    Springer
    Monatshefte für Chemie 125 (1994), S. 167-188 
    Details
    ISSN: 1434-4475
    Keywords: Inverse folding ; parallel computing ; public domain software ; RNA folding ; RNA secondary structures ; tree editing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die im Vienna RNA package enthaltenen Computer Programme für die Berechnung und den Vergleich von RNA Sekundärstrukturen werden präsentiert. Ihren Kern bilden Algorithmen zur Vorhersage von Strukturen minimaler Energie sowie zur Berechnung von Zustandssumme und Basenpaarungswahrscheinlichkeiten mittels dynamischer Programmierung. Ein effizienter heuristischer Algorithmus für das inverse Faltungsproblem wird vorgestellt. Darüberhinaus präsentieren wir kompakte und effiziente Programme zum Vergleich von RNA Sekundärstrukturen durch Baum-Editierung und Alignierung. Alle Programme sind in ANSI C geschrieben, darunter auch eine Implementation des Faltungs-algorithmus für Parallelrechner mit verteiltem Speicher. Wie Tests auf einem Intel Hypercube zeigen, wird das Parallelrechnen umso effizienter je länger die Sequenzen sind.
    Notes: Summary Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities. An efficient heuristic for the inverse folding problem of RNA is introduced. In addition we present compact and efficient programs for the comparison of RNA secondary structures based on tree editing and alignment. All computer codes are written in ANSI C. They include implementations of modified algorithms on parallel computers with distributed memory. Performance analysis carried out on an Intel Hypercube shows that parallel computing becomes gradually more and more efficient the longer the sequences are.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00818163
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  • 4
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    RNA multi-structure landscapes (1993)
    Springer
    Details
    Publication Date: 1993-04-01
    Print ISSN: 0175-7571
    Electronic ISSN: 1432-1017
    Topics: Biology , Physics
    Published by Springer
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