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Figure 1 | BMC Evolutionary Biology

Figure 1

From: Collective properties of evolving molecular quasispecies

Figure 1

Heterogeneity of sequences and structures, and quantities related. Examples of RNA sequences (written in 5'-3' orientation) and their corresponding structures in bracket notation at the statistically stationary state of a numerical simulation with N = 602, n = 35, μ = 0.0325. The probability that a sequence folds into the target structure (a hammerhead structure, represented in the upper right corner) is ρ ¯ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacuWFbpGCgaqeaaaa@2E8B@ = 0.25. Other densities are ρ ¯ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacuWFbpGCgaqeaaaa@2E8B@ C = 0.85, ρ ¯ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacuWFbpGCgaqeaaaa@2E8B@ S = 0.99, and ρ ¯ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaaiiGacuWFbpGCgaqeaaaa@2E8B@ M = 0.01. At the time step chosen, the structure of the consensus sequence and the consensus structure differ in one position, and the latter does not correspond to any real secondary RNA structure (a very rare event in the asymptotic regime, but shown here for illustration). The Hamming distance between the sequences shown and the consensus sequence varies from 8 to 15, and does not show any significant difference whether the sequence folds into the target structure or whether the corresponding structure is rare (last group). Despite a well defined global state where the population, as a whole, clearly contains all the information on the target structure, both the density of sequences folding into it and especially the density of the most abundant sequence present low values.

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