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On DNA numerical representations for genomic similarity computation.

ABSTRACT: 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.

SUBMITTER: Mendizabal-Ruiz G

PROVIDER: S-EPMC5360225 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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On DNA numerical representations for genomic similarity computation.

Mendizabal-Ruiz Gerardo G Román-Godínez Israel I Torres-Ramos Sulema S Salido-Ruiz Ricardo A RA Morales J Alejandro JA

PloS one 20170321 3

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 th ...[more]

PMID: 28323839

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