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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.


Depiction of phylogenetic trees for the ribosomal 18S subunit gene of 26 selected species.(A and B) Trees computed with GAFD and NW, respectively. (C) Maximum parsimony-bootstrapped Phylip tree. The species assessed and their corresponding KEGG entries are: Acyrthosiphon pisum (api:100145839), Aedes aegypti (aag:AaeL_AAEL009747), Apis mellifera (ame:552726), Bos taurus (bta:326602), Caenorrhabditis elegans (cel:Y57G11C.16), Canis familiaris (cfa:403685), Ciona intestinalis (cin:100182116), Danio rerio (dre:192300), Drosophila melanogaster (dme:Dmel_CG8900), Equus caballus (ecb:100052654), Homo sapiens (hsa:6222), Macaca mulatta (mcc:713939), Monodelphis domestica (mdo:100027117), Mus musculus (mmu:20084), Nasonia vitripennis (nvi:100117049), Nematostella vectensis (nve:NEMVE_v1g245261), Oryza sativa (osa:4334407), Pan troglodytes (ptr:455055), Populus trichocarpa (pop:POPTR_551159), Rattus norvegicus (rno:100360679), Ricinus communis (rcu:RCOM_0557270), Saccharomyces cerevisiae (sce:YDR450W), Sus scrofa (ssc:396980), Vitis vinifera (vvi:100245272), Xenopus tropicalis (xla:414719), Zea mays (zma:100285246). The trees are color-coded for the relevant phylogenetic groups, namely blue for eutherian mammals, green for plants and brown for insects. S. cerevisiae is bolded as reference.
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pone-0110954-g003: Depiction of phylogenetic trees for the ribosomal 18S subunit gene of 26 selected species.(A and B) Trees computed with GAFD and NW, respectively. (C) Maximum parsimony-bootstrapped Phylip tree. The species assessed and their corresponding KEGG entries are: Acyrthosiphon pisum (api:100145839), Aedes aegypti (aag:AaeL_AAEL009747), Apis mellifera (ame:552726), Bos taurus (bta:326602), Caenorrhabditis elegans (cel:Y57G11C.16), Canis familiaris (cfa:403685), Ciona intestinalis (cin:100182116), Danio rerio (dre:192300), Drosophila melanogaster (dme:Dmel_CG8900), Equus caballus (ecb:100052654), Homo sapiens (hsa:6222), Macaca mulatta (mcc:713939), Monodelphis domestica (mdo:100027117), Mus musculus (mmu:20084), Nasonia vitripennis (nvi:100117049), Nematostella vectensis (nve:NEMVE_v1g245261), Oryza sativa (osa:4334407), Pan troglodytes (ptr:455055), Populus trichocarpa (pop:POPTR_551159), Rattus norvegicus (rno:100360679), Ricinus communis (rcu:RCOM_0557270), Saccharomyces cerevisiae (sce:YDR450W), Sus scrofa (ssc:396980), Vitis vinifera (vvi:100245272), Xenopus tropicalis (xla:414719), Zea mays (zma:100285246). The trees are color-coded for the relevant phylogenetic groups, namely blue for eutherian mammals, green for plants and brown for insects. S. cerevisiae is bolded as reference.

Mentions: Two experiments were performed by analyzing two sets of DNA sequences corresponding to the ribosomal S18 subunit (KEGG orthology K02964). This gene was selected because it is the broadest evolutionary marker discernable between all eukaryotes. In the first experiment, three basic clusters were built, namely mammals, insects, and plants, according to general taxonomy. The resulting phylogenetic trees generated from the distance matrices computed by the three methods are depicted in Figure 3. Note that the eutheryan (a mammal subgroup) were grouped in GAFD, NW, and Phylip. However, the insects were grouped differently by the three methods (e.g., Nasonia vitripennis was located far outside the other insects according to GAFD and Phylip). These results are consistent with the known complexity of insect genetics due to horizontal transference, spurious recombination, and high variability rate. Note that NW represented the outside eukaryote Saccharomyces cerevisiae appropriately, while GAFD placed it incorrectly among the plant group. Phylip placed this sequence in an outer group next to Monodelphis domestica and N. vitripennis. Although M. domestica was expected to be placed in an external group within mammals, it was placed in the outer branch of all trees. Lastly, with the exception of S. cerevisiae in GAFD, all plants were properly clustered.


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)

Depiction of phylogenetic trees for the ribosomal 18S subunit gene of 26 selected species.(A and B) Trees computed with GAFD and NW, respectively. (C) Maximum parsimony-bootstrapped Phylip tree. The species assessed and their corresponding KEGG entries are: Acyrthosiphon pisum (api:100145839), Aedes aegypti (aag:AaeL_AAEL009747), Apis mellifera (ame:552726), Bos taurus (bta:326602), Caenorrhabditis elegans (cel:Y57G11C.16), Canis familiaris (cfa:403685), Ciona intestinalis (cin:100182116), Danio rerio (dre:192300), Drosophila melanogaster (dme:Dmel_CG8900), Equus caballus (ecb:100052654), Homo sapiens (hsa:6222), Macaca mulatta (mcc:713939), Monodelphis domestica (mdo:100027117), Mus musculus (mmu:20084), Nasonia vitripennis (nvi:100117049), Nematostella vectensis (nve:NEMVE_v1g245261), Oryza sativa (osa:4334407), Pan troglodytes (ptr:455055), Populus trichocarpa (pop:POPTR_551159), Rattus norvegicus (rno:100360679), Ricinus communis (rcu:RCOM_0557270), Saccharomyces cerevisiae (sce:YDR450W), Sus scrofa (ssc:396980), Vitis vinifera (vvi:100245272), Xenopus tropicalis (xla:414719), Zea mays (zma:100285246). The trees are color-coded for the relevant phylogenetic groups, namely blue for eutherian mammals, green for plants and brown for insects. S. cerevisiae is bolded as reference.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0110954-g003: Depiction of phylogenetic trees for the ribosomal 18S subunit gene of 26 selected species.(A and B) Trees computed with GAFD and NW, respectively. (C) Maximum parsimony-bootstrapped Phylip tree. The species assessed and their corresponding KEGG entries are: Acyrthosiphon pisum (api:100145839), Aedes aegypti (aag:AaeL_AAEL009747), Apis mellifera (ame:552726), Bos taurus (bta:326602), Caenorrhabditis elegans (cel:Y57G11C.16), Canis familiaris (cfa:403685), Ciona intestinalis (cin:100182116), Danio rerio (dre:192300), Drosophila melanogaster (dme:Dmel_CG8900), Equus caballus (ecb:100052654), Homo sapiens (hsa:6222), Macaca mulatta (mcc:713939), Monodelphis domestica (mdo:100027117), Mus musculus (mmu:20084), Nasonia vitripennis (nvi:100117049), Nematostella vectensis (nve:NEMVE_v1g245261), Oryza sativa (osa:4334407), Pan troglodytes (ptr:455055), Populus trichocarpa (pop:POPTR_551159), Rattus norvegicus (rno:100360679), Ricinus communis (rcu:RCOM_0557270), Saccharomyces cerevisiae (sce:YDR450W), Sus scrofa (ssc:396980), Vitis vinifera (vvi:100245272), Xenopus tropicalis (xla:414719), Zea mays (zma:100285246). The trees are color-coded for the relevant phylogenetic groups, namely blue for eutherian mammals, green for plants and brown for insects. S. cerevisiae is bolded as reference.
Mentions: Two experiments were performed by analyzing two sets of DNA sequences corresponding to the ribosomal S18 subunit (KEGG orthology K02964). This gene was selected because it is the broadest evolutionary marker discernable between all eukaryotes. In the first experiment, three basic clusters were built, namely mammals, insects, and plants, according to general taxonomy. The resulting phylogenetic trees generated from the distance matrices computed by the three methods are depicted in Figure 3. Note that the eutheryan (a mammal subgroup) were grouped in GAFD, NW, and Phylip. However, the insects were grouped differently by the three methods (e.g., Nasonia vitripennis was located far outside the other insects according to GAFD and Phylip). These results are consistent with the known complexity of insect genetics due to horizontal transference, spurious recombination, and high variability rate. Note that NW represented the outside eukaryote Saccharomyces cerevisiae appropriately, while GAFD placed it incorrectly among the plant group. Phylip placed this sequence in an outer group next to Monodelphis domestica and N. vitripennis. Although M. domestica was expected to be placed in an external group within mammals, it was placed in the outer branch of all trees. Lastly, with the exception of S. cerevisiae in GAFD, all plants were properly clustered.

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.