Identification of protein coding regions using the modified Gabor-wavelet transform

by J. P. Mena-Chalco, H. Carrer, Y. Zana, and R. M. Cesar-Jr. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5:198-207, 2008.

An important topic in genomic sequence analysis is the identification of protein coding regions. In this context, several coding DNA model-independent methods, based on the occurrence of specific patterns of nucleotides at coding regions, have been proposed. Nonetheless, these methods have not been completely suitable due to their dependence on an empirically pre-defined window length required for a local analysis of a DNA region.
We introduce a method, based on a modified Gabor-wavelet transform (MGWT), for the identification of protein coding regions. This novel transform is tuned to analyze periodic signal components and presents the advantage of being independent of the window length. We compared the performance of the MGWT with other methods using eukaryote datasets. The results show that the MGWT outperforms all assessed model-independent methods with respect to identification accuracy. These results indicate that the source of at least part of the identification errors produced by the previous methods is the fixed working scale. The new method not only avoids this source of errors, but also makes available a tool for detailed exploration of the nucleotide occurrence.

J. P. Mena-Chalco
Last modified: Fri Sep 14 01:40:42 BRT 2007