Abstract
Evidence seems to show that coding DNA is more random than noncoding DNA, but other conflicting evidence also exists. Based on the third-base degeneracy of codons, we regard the third position of codons as a ‘noisy’ position. By deleting one fixed position of non-overlapping triplets in a given sequence, three masked sequences may be deduced from the sequence. We have investigated the block-to-site mutual information functions of coding and noncoding sequences in yeast without and with the masking. Characteristics that distinguish coding from noncoding DNA have been found. It is observed that the strong correlations in the coding regions may be blocked by the third base of codons, and the proper masking can extract the correlations. Distribution of dimeric tandem repeats of unmasked sequences is also compared with that of masked sequences.
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