On DNA numerical representations for genomic similarity computation.
Genomic signal processing (GSP) refers to the use of signal processing for the analysis of genomic data. GSP methods require the transformation or mapping of the genomic data to a numeric representation. To date, several DNA numeric representations (DNR) have been proposed; however, it is not clear what the properties of each DNR are and how the selection of one will affect the results when using a signal processing technique to analyze them. In this paper, we present an experimental study of the characteristics of nine of the most frequently-used DNR. The objective of this paper is to evaluate the behavior of each representation when used to measure the similarity of a given pair of DNA sequences.
Departamento de Ciencias Computacionales, División de Electrónica y Computación, Universidad de Guadalajara, Guadalajara, Jalisco, México.
Gerardo
G
Mendizabal-Ruiz
Departamento de Ciencias Computacionales, División de Electrónica y Computación, Universidad de Guadalajara, Guadalajara, Jalisco, México.
Israel
I
Román-Godínez
Departamento de Ciencias Computacionales, División de Electrónica y Computación, Universidad de Guadalajara, Guadalajara, Jalisco, México.
Sulema
S
Torres-Ramos
Departamento de Ciencias Computacionales, División de Electrónica y Computación, Universidad de Guadalajara, Guadalajara, Jalisco, México.
Ricardo A
RA
Salido-Ruiz
Departamento de Ciencias Computacionales, División de Electrónica y Computación, Universidad de Guadalajara, Guadalajara, Jalisco, México.
J Alejandro
JA
Morales
D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D051545:Cyclooxygenase 1 / Q000235:genetics; D030541:Databases, Genetic; D006801:Humans; D012269:Ribosomal Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D017385:Sequence Homology; D012815:Signal Processing, Computer-Assisted
D012269:Ribosomal Proteins; C041184:ribosomal protein S18; D051545:Cyclooxygenase 1