The ribosome as a table-driven convolutional decoder for the Escherichia coli K-12 translation initiation system

Elebeoba May; M. A. Vouk; D. L. Bitzer; D. I. Rosnick

The ribosome as a table-driven convolutional decoder for the Escherichia coli K-12 translation initiation system

Elebeoba May, M. A. Vouk, D. L. Bitzer, D. I. Rosnick

Research output: Contribution to journal › Conference article › peer-review

Abstract

Redundancy occurs naturally within RNA and DNA sequences [1]. The existence of tandem repeats, and sequences such as the Shine-Dalgarno sequence, the Pribnow box and the TATA box, leads us to believe that cellular communication systems use some method of coding to recognize valid information regions within a nucleotide sequence and correct for "transmission" errors such as mutations. In this paper we use principles of convolutional coding theory to analyze the translation initiation process. The principle hypothesis is that the messenger RNA (mRNA) sequence can be viewed as a noisy, convolutionaly encoded signal. The ribosome is functionally paralleled to a table-driven convolutional decoder. The 16s ribosomal RNA (rRNA) sequence is used to form decoding masks for table-driven decoding. The results of applying this method to Escherichia coli K-12 strain MG1655 are presented.

Original language	English (US)
Pages (from-to)	2466-2469
Number of pages	4
Journal	Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
Volume	4
State	Published - Dec 1 2000
Event	22nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Chicago, IL, United States Duration: Jul 23 2000 → Jul 28 2000

Keywords

Coding theory
Convolutional codes
Table-driven codes
Translation initiation

ASJC Scopus subject areas

Signal Processing
Biomedical Engineering
Computer Vision and Pattern Recognition
Health Informatics

Cite this

The ribosome as a table-driven convolutional decoder for the Escherichia coli K-12 translation initiation system. / May, Elebeoba; Vouk, M. A.; Bitzer, D. L. et al.

In: Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings, Vol. 4, 01.12.2000, p. 2466-2469.

Research output: Contribution to journal › Conference article › peer-review

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AU - Rosnick, D. I.

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AB - Redundancy occurs naturally within RNA and DNA sequences [1]. The existence of tandem repeats, and sequences such as the Shine-Dalgarno sequence, the Pribnow box and the TATA box, leads us to believe that cellular communication systems use some method of coding to recognize valid information regions within a nucleotide sequence and correct for "transmission" errors such as mutations. In this paper we use principles of convolutional coding theory to analyze the translation initiation process. The principle hypothesis is that the messenger RNA (mRNA) sequence can be viewed as a noisy, convolutionaly encoded signal. The ribosome is functionally paralleled to a table-driven convolutional decoder. The 16s ribosomal RNA (rRNA) sequence is used to form decoding masks for table-driven decoding. The results of applying this method to Escherichia coli K-12 strain MG1655 are presented.

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The ribosome as a table-driven convolutional decoder for the Escherichia coli K-12 translation initiation system

Abstract

Keywords

ASJC Scopus subject areas

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