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The second phase of ice advance led to the accretion of a relatively simple thrust and folded sequence seen the northern side of Mud Buttes.
The Sanchez Eby theory extends Flory's treatment of final melting temperature to metastable folded sequence crystals of arbitrary thickness lmax, and also allows for incorporation of B units in the crystal.
The reason is that the partial folded sequence forms its structural frame.
The Gibbs free energy (E) of a (folded) sequence defines the probability of the sequence being in the folded state (pfold, Eq. 1).. Replicability, enzymatic activity and replicator degradation rate are responsible for the dynamics of the system.
For PKNOTS data set, we preprocess the sequence with the first step of GM and then obtain the output of the partially folded sequence as the input of the PKNOTS and LZ algorithms.
This provides a summary of all data gathered for a given sequence including: background information on the gene and location of the -1 PRF signal, information regarding the program used to perform the MFE prediction, multiple methods to view the secondary structure, and a comparison of the distribution of randomized sequences to the MFE of the folded sequence.
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The folded sequences were then input into the MirCheck program [ 1] to check their secondary structures.
As an alternative, we also used RNAifold to generate inverse folded sequences.
Subsequently, we obtain the partially folded sequences as the input of PKONTS and LZ algorithm and run them with the same energy model and parameters as above.
Mutational robustness of S is calculated by comparing its neutrality to the mean neutrality of 100 inverse folded sequences (Equation 17).
The folded sequences generated were then checked to see if the sRNA (putative mature miRNA obtained by sequencing) occurs in the folded putative precursor as the window scanning approach used could report a folded structure not involving the concerned sRNA.
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