An error-correcting code framework for genetic sequence analysis

• Published in: Journal of the Franklin Institute Vol. 341; no. 1; pp. 89 - 109
• Main Authors: May, Elebeoba E., Vouk, Mladen A., Bitzer, Donald L., Rosnick, David I.
• Format: Journal Article Conference Proceeding
• Language: English
• Published: Oxford Elsevier Ltd 2004; Elsevier
• Subjects: Analytical biochemistry: general aspects, technics, instrumentation; Analytical, structural and metabolic biochemistry; Applied sciences; Biological and medical sciences; Biological coding theory; Coding theory; Computer science; control theory; systems; Error-correcting codes; Exact sciences and technology; Fundamental and applied biological sciences. Psychology; Information systems. Data bases; Information theory; Memory organisation. Data processing; Software; Translation initiation; Biological coding theory; Error-correcting codes; Coding theory; Translation initiation; Information theory; Genetic algorithm; Coding; Systems engineering; Error correcting code; Molecular biology; Information transmission; Biological system
• ISSN: 0016-0032; 1879-2693
• DOI: 10.1016/j.jfranklin.2003.12.009

A fundamental challenge for engineering communication systems is the problem of transmitting information from the source to the receiver over a noisy channel. This same problem exists in a biological system. How can information required for the proper functioning of a cell, an organism, or a species be transmitted in an error introducing environment? Source codes (compression codes) and channel codes (error-correcting codes) address this problem in engineering communication systems. The ability to extend these information theory concepts to study information transmission in biological systems can contribute to the general understanding of biological communication mechanisms and extend the field of coding theory into the biological domain. In this work, we review and compare existing coding theoretic methods for modeling genetic systems. We introduce a new error-correcting code framework for understanding translation initiation, at the cellular level and present research results for Escherichia coli K-12. By studying translation initiation, we hope to gain insight into potential error-correcting aspects of genomic sequences and systems.