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

• Main Authors: HyoYoung Kim, Samsun Sung, Seoae Cho, Tae-Hun Kim, Kangseok Seo, Heebal Kim
• Format: Article
• Language: English
• Published: Asian-Australasian Association of Animal Production Societies 2014-12-01
• Series: Asian-Australasian Journal of Animal Sciences
• Subjects: Copy Number Variation; Cytomap; Homozygosity; Single Nucleotide Polymorphism; Visualization
• Online Access: http://www.ajas.info/upload/pdf/ajas-27-12-1691.pdf

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.