An error-correcting code framework for genetic sequence analysis

@article{citeulike:1053001, 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.}, author = {May, Elebeoba E. and Vouk, Mladen A. and Bitzer, Donald L. and Rosnick, David I. }, booktitle = {Genomics, Signal Processing, and Statistics}, citeulike-article-id = {1053001}, doi = {http://dx.doi.org/10.1016/j.jfranklin.2003.12.009}, journal = {Journal of the Franklin Institute}, keywords = {dna, error-correction, information-theory}, month = {}, number = {1-2}, pages = {89--109}, posted-at = {2007-01-19 15:23:20}, priority = {1}, title = {An error-correcting code framework for genetic sequence analysis}, url = {http://dx.doi.org/10.1016/j.jfranklin.2003.12.009}, volume = {341}, year = {2004} }

TY - JOUR ID - citeulike:1053001 L3 - citeulike-article-id:1053001 N2 - 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. IS - 1-2 JF - Journal of the Franklin Institute EP - 109 TI - An error-correcting code framework for genetic sequence analysis VL - 341 T2 - Genomics, Signal Processing, and Statistics SP - 89 KW - dna KW - error-correction KW - information-theory AU - May, Elebeoba AU - Vouk, Mladen AU - Bitzer, Donald AU - Rosnick, David PY - 2004/0// UR - http://dx.doi.org/10.1016/j.jfranklin.2003.12.009 ER -