SNPViz - Visualization of SNPs in proteins

Visualization of SNPs with t-SNE

BACKGROUND Single Nucleotide Polymorphisms (SNPs) are one of the largest sources of new data in biology. In most papers, SNPs between individuals are visualized with Principal Component Analysis (PCA), an older method for this purpose. PRINCIPAL FINDINGS We compare PCA, an aging method for this purpose, with a newer method, t-Distributed Stochastic Neighbor Embedding (t-SNE) for the visualiza...

Presence of SNPs in GDF9 mRNA of Iranian Afshari Sheep

Identification and visualization of cage-shaped proteins

UNLABELLED Cage-shaped protein, with its special structure, may have potential applications in biomedicine and nanotechnology. We developed a program CSPro (Cage-Shaped Protein) for efficient identification of cage-shaped proteins based on quaternary structure. CSPro is capable of revealing the corresponding cage-shaped feature more clearly and quickly than traditional visualization tools. Usin...

Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies

The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive ...

Live In-Cell Visualization of Proteins Using Super Resolution Imaging