title: Identification of protein coding regions using the modified Gabor-wavelet transform.
abstract: 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.
authors.affiliation: Departmento de Ciencia da Computação, Instituto de Matemática e Estatística de Universidade de São Paulo, Rua do Matão, Cidade Universitária, São Paulo, SP, Brasil. jmena@vision.ime.usp.br
authors.forename: Jesús P
authors.initials: JP
authors.lastname: Mena-Chalco
authors.forename: Helaine
authors.initials: H
authors.lastname: Carrer
authors.forename: Yossi
authors.initials: Y
authors.lastname: Zana
authors.forename: Roberto M
authors.initials: RM
authors.lastname: Cesar
mesh_terms: D019295:Computational Biology; D004247:DNA / Q000235:genetics*; D030561:Databases, Nucleic Acid; D030562:Databases, Protein; D005914:Globins / Q000235:genetics; D006801:Humans; D015233:Models, Statistical; D010363:Pattern Recognition, Automated; D011506:Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data*; D012815:Signal Processing, Computer-Assisted
chemical_list: D011506:Proteins; D005914:Globins; D004247:DNA