An error-correcting code framework for genetic sequence analysis

Elebeoba E. May, Mladen A. Vouk, Donald L. Bitzer, David I. Rosnick

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

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. Published by Elsevier Ltd. on behalf of The Franklin Institute.

Original languageEnglish (US)
Pages (from-to)89-109
Number of pages21
JournalJournal of the Franklin Institute
Volume341
Issue number1-2
DOIs
StatePublished - Jan 2004

Keywords

  • Biological coding theory
  • Coding theory
  • Error-correcting codes
  • Information theory
  • Translation initiation

ASJC Scopus subject areas

  • Modeling and Simulation
  • Control and Optimization
  • Applied Mathematics
  • Electrical and Electronic Engineering
  • Control and Systems Engineering
  • Information Systems and Management
  • Signal Processing

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