Limits...
Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

Borrayo E, Mendizabal-Ruiz EG, Vélez-Pérez H, Romo-Vázquez R, Mendizabal AP, Morales JA - PLoS ONE (2014)

Bottom Line: We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal.Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments.Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

View Article: PubMed Central - PubMed

Affiliation: Computer Sciences Department, CUCEI - Universidad de Guadalajara, Guadalajara, México.

ABSTRACT
Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

No MeSH data available.


Examples of the resulting DNA sequence-to-signal tool employing different values of α and its effects on single sequence changes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4230918&req=5

pone-0110954-g001: Examples of the resulting DNA sequence-to-signal tool employing different values of α and its effects on single sequence changes.

Mentions: Given that our proposed DNA sequence-to-signal mapping accounts for neighboring nucleotides, small differences between and due to indels and mutations produce a shift in the intensity of the resulting signal (Fig. 1). To account for these changes, we compared the derivatives of the two signals by using finite differences and computed the mean slope as a descriptor representing the degree of similarity between the two signals. A value indicates strong similarity.


Genomic signal processing methods for computation of alignment-free distances from DNA sequences.

Borrayo E, Mendizabal-Ruiz EG, Vélez-Pérez H, Romo-Vázquez R, Mendizabal AP, Morales JA - PLoS ONE (2014)

Examples of the resulting DNA sequence-to-signal tool employing different values of α and its effects on single sequence changes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230918&req=5

pone-0110954-g001: Examples of the resulting DNA sequence-to-signal tool employing different values of α and its effects on single sequence changes.
Mentions: Given that our proposed DNA sequence-to-signal mapping accounts for neighboring nucleotides, small differences between and due to indels and mutations produce a shift in the intensity of the resulting signal (Fig. 1). To account for these changes, we compared the derivatives of the two signals by using finite differences and computed the mean slope as a descriptor representing the degree of similarity between the two signals. A value indicates strong similarity.

Bottom Line: We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal.Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments.Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

View Article: PubMed Central - PubMed

Affiliation: Computer Sciences Department, CUCEI - Universidad de Guadalajara, Guadalajara, México.

ABSTRACT
Genomic signal processing (GSP) refers to the use of digital signal processing (DSP) tools for analyzing genomic data such as DNA sequences. A possible application of GSP that has not been fully explored is the computation of the distance between a pair of sequences. In this work we present GAFD, a novel GSP alignment-free distance computation method. We introduce a DNA sequence-to-signal mapping function based on the employment of doublet values, which increases the number of possible amplitude values for the generated signal. Additionally, we explore the use of three DSP distance metrics as descriptors for categorizing DNA signal fragments. Our results indicate the feasibility of employing GAFD for computing sequence distances and the use of descriptors for characterizing DNA fragments.

No MeSH data available.