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VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

  • Kim, HyoYoung (Department of Agricultural Biotechnology, Seoul National University) ;
  • Sung, Samsun (CHO&KIM Genomics, Seoul National University Research Park) ;
  • Cho, Seoae (CHO&KIM Genomics, Seoul National University Research Park) ;
  • Kim, Tae-Hun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Seo, Kangseok (Animal Genetic Evaluation Division, National Livestock Research Institute, RDA) ;
  • Kim, Heebal (Department of Agricultural Biotechnology, Seoul National University)
  • Received : 2014.02.25
  • Accepted : 2014.06.21
  • Published : 2014.12.01

Abstract

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

Keywords

Copy Number Variation;Cytomap;Homozygosity;Single Nucleotide Polymorphism;Visualization

Acknowledgement

Supported by : Rural Development Administration

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