D. L. Bitzer

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This work gives a brief overview of information theory based approaches to genetic sequence and system analysis. The state of research with regard to error-correction coding theory methods for evaluating the genetic translation initiation system is explored. We present research results of interest in the area of error-control coding methods for modeling the(More)
The free energy released during the interaction of the 16S rRNA tail with the mRNA sequence during translation contains a weak sinusoidal pattern of frequency 1/3 cycles/nucleotide. We hypothesize that this signal encodes information related to the maintenance of reading frame during elongation. In the case of the well-studied +1 frameshifter, prfB in E.(More)
In Prokaryotes, free energy based calculations of the binding interaction between their 16S rRNA tail end and their underlying mRNA has been used to analyze the translation process. There have been examinations of the free-energy interaction between the 16S rRNA and mRNA with focus on the leader region. The focus on the leader region has revealed an(More)
Interactions of the ribosome with the mRNA constitute the mechanism of translation in bacteria. We hypothesize that a variable free energy pattern arising from repeated hybridizations of the rRNA tail with a moving window of mRNA sequence could encode information required to maintain translational reading frame. If present, this signal should exist in all(More)
The exact identification of splice sites is a major functional sequence mapping task. The interaction between pre-mRNA splice sites and snRNAs suggests that thermodynamic models could provide methods for identifying splice sites. We show that the donor site position can be identified by finding the minimum binding energy calculated between a mask(More)
In prokaryotes, Shine-Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis by allowing the two molecules to hybridize and form a double-helix. Many mRNAs, however, lack SD sequences and presumably use another mechanism to(More)
The 16s ribosomal tail has been conjectured to play an important role in the regulation of protein production. In previous work, we generated sequences of 13 base pairs as hypothetical ribosome tail ends for E. coli K-12. We found the actual E. coli ribosome tail to be significantly different from a randomly generated one in the magnitude of the lock and(More)
Free energy calculation for binding between the Shine-Dalgarno 3' end of the 16S rRNA and initiation sites in E.coli suggest the region is used as an landing site for construction of the ribosome around mRNA. Research indicates that there is a continued role for Shine-Dalgarno interaction within coding sequences – a mechanism that is still unclear. The(More)
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