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Welcome to the PhenGenVar Browser website.

The PhenGenVar browser is a desktop application for interactively browsing genomic, genetic and phenotypic data in the context of a reference genome. Our key strategies include the use of phenotype-to-genotype (PhenGenVar) knowledge-base, enabling efficient visualization and exploration of disease-gene-variants relationships, even for the large-scale data analysis. It allows users to flexibly browse the genomic regions and the variants associated with a specific phenotype. For instance, selecting a specific phenotype and then choosing a gene (transcript) from the phenotype-related gene list will display the corresponding genomic regions with the reported variants. Additionally, the Genome Browser can be called from the Exome Browser and utilized to closely browse the variant calling results based on read alignment. The PhenGenVar browser allows users to efficiently detect disease-gene-variant relationships by using the disease-specific knowledge-base, while providing a convenient and intuitive user interface at various levels of genomic resolution. Contact: Jeehee Yoon (jhyoon@hallym.ac.kr) and Jaemoon Shin (shin@dbcls.rois.ac.jp)  (If you have any requirements and advices, freely let us know).

Simple steps to use PhenGenVar Browser (1) Load a BAM file and a VCF file containing variant calling results (optional) by selecting them using the File menu. Note: select only BAM and VCF files that have index files (*.bai/*.idx). (2) Select a reference sequence version and a dbSNP version (optional) which are necessary for BAM/VCF file analysis. (3) Select a Gene_Group or Phenotype to analyze. The related gene sets are displayed in the Gene/Transcript View area. (4) Double click a random gene output in the Gene/Transcript View area to obtain the transcript data of the gene in a child node. If a random transcript is double-clicked, the variant information areas are activated to provide the variant list identified on the transcript of interest. (5) Select and click a random variant to display an exon area including the position of the selected variant in the Main Exon View Panel. (6) Select a variant and double click with a mouse to call a Genome Browser centering at the position of the related variant and use it for a detailed analysis of that area.

Database Laboratory, Department of Computer Engineering, Hallym University, 1 Hallymdaehak-gil, Chuncheon, Gangwon-do 200-702, Korea