BioMed Research International

BioMed Research International / 2005 / Article
Special Issue

Data Mining in Genomics and Proteomics

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Research article | Open Access

Volume 2005 |Article ID 371096 | 8 pages |

Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences

Received24 May 2004
Revised30 Aug 2004
Accepted03 Sep 2004


Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized as a random fractal. When a gene-finding algorithm incorporates multiple sources of information about coding regions, it becomes more successful. It is thus highly desirable to develop new and efficient codon indices by simultaneously characterizing the fractal and periodic features of a DNA sequence. In this paper, we describe a novel way of achieving this goal. The efficiency of the new codon index is evaluated by studying all of the 16 yeast chromosomes. In particular, we show that the method automatically and correctly identifies which of the three reading frames is the one that contains a gene.

Copyright © 2005 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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