The Human Genome Project promises to generate a huge datastream of DNA sequences for which computational tools are needed for analysis. Human DNA or mRNA sequences coding for expressed genes will be of biomedical interest for genetic diseases or therapeutic polypeptides. An examination of mRNA sequences in GENBANK has revealed that calculated mRNA folding is more stable than expected by chance. Free energy minimization calculations of small native mRNA sequences are more negative than randomized mRNA sequences of the same composition. This suggests a bias in codon choice that favors mRNA structures which have greater folding stability. This research will address the following question: Is there a difference in folding stability bias between small and large mRNA molecules? Small mRNAs have been shown to be biased toward more negative folding free energies. Do larger mRNAs also exhibit this property?
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