Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes

William J. Faison, Alexandre Rostovtsev, Eduardo Castro-Nallar, Keith A. Crandall, Konstantin Chumakov, Vahan Simonyan, Raja Mazumder

Resultado de la investigación: Article

9 Citas (Scopus)

Resumen

Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the samples. However, in practice this is difficult because currently there is no stand-alone tool that takes SNP data directly as input and produces phylogenetic trees. In response to this need, PhyloSNP application was created with two analysis methods 1) a quantitative method that creates the presence/absence matrix which can be directly used to generate phylogenetic trees or creates a tree from a shrunk genome alignment (includes additional bases surrounding the SNP position) and 2) a qualitative method that clusters samples based on the frequency of different bases found at a particular position. The algorithms were used to generate trees from Poliovirus, Burkholderia and human cancer genomics NGS datasets.Availability: PhyloSNP is freely available for download at http://hive.biochemistry.gwu.edu/dna.cgi?cmd=phylosnp.

Idioma originalEnglish
Páginas (desde-hasta)1-7
Número de páginas7
PublicaciónGenomics
Volumen104
N.º1
DOI
EstadoPublished - 2014

Huella dactilar

Bacterial Genomes
Viral Genome
Human Genome
Single Nucleotide Polymorphism
Nucleotides
Genome
Burkholderia
Poliovirus
Urticaria
Genomics
Biochemistry
Neoplasms

ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Citar esto

Faison, William J. ; Rostovtsev, Alexandre ; Castro-Nallar, Eduardo ; Crandall, Keith A. ; Chumakov, Konstantin ; Simonyan, Vahan ; Mazumder, Raja. / Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. En: Genomics. 2014 ; Vol. 104, N.º 1. pp. 1-7.
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Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes. / Faison, William J.; Rostovtsev, Alexandre; Castro-Nallar, Eduardo; Crandall, Keith A.; Chumakov, Konstantin; Simonyan, Vahan; Mazumder, Raja.

En: Genomics, Vol. 104, N.º 1, 2014, p. 1-7.

Resultado de la investigación: Article

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AU - Rostovtsev, Alexandre

AU - Castro-Nallar, Eduardo

AU - Crandall, Keith A.

AU - Chumakov, Konstantin

AU - Simonyan, Vahan

AU - Mazumder, Raja

PY - 2014

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AB - Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the samples. However, in practice this is difficult because currently there is no stand-alone tool that takes SNP data directly as input and produces phylogenetic trees. In response to this need, PhyloSNP application was created with two analysis methods 1) a quantitative method that creates the presence/absence matrix which can be directly used to generate phylogenetic trees or creates a tree from a shrunk genome alignment (includes additional bases surrounding the SNP position) and 2) a qualitative method that clusters samples based on the frequency of different bases found at a particular position. The algorithms were used to generate trees from Poliovirus, Burkholderia and human cancer genomics NGS datasets.Availability: PhyloSNP is freely available for download at http://hive.biochemistry.gwu.edu/dna.cgi?cmd=phylosnp.

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