P. Schuster, "Genotypes with phenotypes. Adventures in an RNA toy world", Biophys.Chem., Vol.66, pp.75-110,1997.  Home/Search   Document Details and Download   Summary   Related Articles   Check

....makes no sense to say that two di#erent sequences have the same structure at atomic resolution. Once we have fixed a level of resolution we implicitly assume that di#erences at finer scales are irrelevant for the dynamic processes at hand. Computational investigations of the GP map of both RNA [24, 25, 26, 27, 28, 29] and proteins [30, 31, 32, 33] show that the coarse graining has far reaching consequences. The coarse graining process defines a partition of the type space X into classes of genotypes with the same phenotype. Not surprisingly, the organization of these classes in genotype space is crucial for ....

Schuster, P. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....(f Gamma g) f may be interpreted as superiority of the structure . A crude estimate for the phenotypic error threshold, at which the dominating phenotype is lost, is obtained by setting = 0: p phen.et. 1 1 Gamma oe n oe n (1 ) 13) A more careful derivation can be found in [88]. It shows that there is critical value = g=f above which all error rates can be tolerated without loosing phenotype. A much more elaborate computation of the phenotypic error threshold can be found in [89] The crude estimate (13) matches the available simulation results within a factor 3. Note ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 1997. in press, Santa Fe Institute preprint 97-04-036.

....# # = f g) f may be interpreted as superiority of the structure #. A crude estimate for the phenotypic error threshold, at which the dominating phenotype is lost, is obtained by setting # = 0: p phen.et. # 1 1 # # # n # # # n (1 #) 13) A more careful derivation can be found in [88]. It shows that there is critical value # = g f above which all error rates can be tolerated without loosing phenotype. A much more elaborate computation of the phenotypic error threshold can be found in [89] The crude estimate (13) matches the available simulation results within a factor 3. ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 1997. in press, Santa Fe Institute preprint 97-04-036.

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P. Schuster, "Genotypes with phenotypes. Adventures in an RNA toy world", Biophys.Chem., Vol.66, pp.75-110,1997.

....(as determined, say, by phylogenetic comparisons) it still captures the logic of constrained base pair optimization characteristic of RNA folding. There is indeed evidence that properties 2 and 3 hold in nature [2, 1 A particular definition of frequent is given by the notion of common [17]: A structure is common, when it its formed by more sequences than the average, #(all sequences) ffi #(all structures) W. Fontana, P. Schuster: Shaping Space Page 5 14] Our claims are further substantiated by observing that the properties we call generic have been found to be insensitive to ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....(as determined, say, by phylogenetic comparisons) it still captures the logic of constrained base pair optimization characteristic of RNA folding. There is indeed evidence that properties 2 and 3 hold in nature [2, 1 A particular definition of frequent is given by the notion of common [17]: A structure is common, when it its formed by more sequences than the average, #(all sequences) # #(all structures) W. Fontana, P. Schuster: Shaping Space Page 5 14] Our claims are further substantiated by observing that the properties we call generic have been found to be insensitive to ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....fitness is a property of the phenotype. The relations between genotypes and phenotypes are thus an intrinsic part of evolution and no theory can be complete without considering them. A comprehensive theory of evolution which is explicitly dealing with phenotypes has been introduced a few years ago [79, 81, 80]. The model is shown in figure 8. The complex process of evolution is partitioned into three simpler phenomena: i) population genetics, ii) migration of populations, and (iii) genotype phenotype mapping. Conventional population genetics is extended by two more aspects: population support ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....(as determined, say, by phylogenetic comparisons) it still captures the logic of constrained base pair optimization characteristic of RNA folding. There is indeed evidence that properties 2 and 3 hold in nature [2, 1 A particular definition of frequent is given by the notion of common [19]: A structure is common, when it its formed by more sequences than the average, #(all sequences) # #(all structures) W. Fontana, P. Schuster: Shaping Space Page 5 16] Our claims are further substantiated by observing that the properties we call generic have been found to be insensitive to ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....accuracy of the algorithm for individual sequences. That is, even if the algorithm fails to reproduce details of the actual secondary structure of a particular sequence (as determined, say, by phylogenetic comparisons) 1 A particular definition of frequent is given by the notion of common [17]: A structure is common, when it its formed by more sequences than the average, #(all sequences) #(all structures) it still captures the logic of constrained base pair optimization characteristic of RNA folding. There is indeed evidence that properties 2 and 3 hold in nature [2, 14] Our ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75--110, 1997.

....tness is a property of the phenotype. The relations between genotypes and phenotypes are thus an intrinsic part of evolution and no theory can be complete without considering them. A comprehensive theory of evolution which is explicitly dealing with phenotypes has been introduced a few years ago [79, 81, 80]. The model is shown in gure 8. The complex process of evolution is partitioned into three simpler phenomena: i) population genetics, ii) migration of populations, and (iii) genotype phenotype mapping. Conventional population genetics is extended by two more aspects: population support dynamics ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75-110, 1997.

....(as determined, say, by phylogenetic comparisons) it still captures the logic of constrained base pair optimization characteristic of RNA folding. There is indeed evidence that properties 2 and 3 hold in nature [2, 1 A particular de nition of frequent is given by the notion of common [19]: A structure is common, when it its formed by more sequences than the average, #(all sequences) #(all structures) W. Fontana, P. Schuster: Shaping Space Page 5 16] Our claims are further substantiated by observing that the properties we call generic have been found to be insensitive to ....

P. Schuster. Genotypes with phenotypes: Adventures in an RNA toy world. Biophys. Chem., 66:75-110, 1997.

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