Free energies of folding for native mRNA sequences are more negative than calculated free energies of folding for randomized mRNA sequences with the same mononucleotide base composition and length. Randomization only of the coding region of most genes also yields folding free energies of less negative magnitude than those of the original mRNA sequences. For 79 mRNA sequences selected from a yeast SAGE library, the free energy minimization calculations of native mRNA sequences are also usually more negative than randomized mRNA sequences, as above. This difference can be expressed as a bias using standard deviation units. We also observed that if this yeast SAGE data is grouped according to expression levels, the mean folding free energy bias is different between the high, average, and low expression-level genes. A t-Test for paired two-samples of means shows a significant difference in folding free energies between high and 175 P.M Pardalos and J. Principe (eds.), Biocomputing,[175][176][177][178][179][180][181][182][183][184]
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