Variant Visualizer Tutorial

submitted by: RGD.Videos

The examination of SNPs has undergone a recent change, and in response to this change, RGD has released the new Variant Visualizer tool (VarVis), taking the place of the old SNPlotyper tool. VarVis is a visualization and analysis tool for sequence variation. The data currently contains 22 rat strains sequenced by 4 independent labs.

Tip of the Week: ChromoHub

submitted by: OpenHelix

Today's tip of the week is on Chromohub, an annotated phylogeny of chromatin mediated signaling genes. For more information, check out our blog post at

: Germline Predictors Of Androgen Deprivation Therapy (ADT) Response In Advanced Prostate Cancer

submitted by: WentzMR
Dr. Manish Kohli, Associate Professor of Medical Oncology at Mayo Clinic in Rochester, MN, discusses his article appearing in the March 2012 issue of Mayo Clinic Proceedings, on the association of the TRMT11 gene and prostate cancer and identifying predictive biomarkers. This research may improve prediction of response to hormonal treatments in advanced prostate cancer patients and potentially enhance delivery of individualized medicine in future patients if the findings are validated....

: Association of TNFSF8 Polymorphisms With Peripheral Neutrophil Count

submitted by: mcgheekkm
Dr. Adelaide Arruda-Olson, Assistant Professor of Medicine in the Cardiovascular Diseases Research Division at Mayo Clinic in Rochester, MN, discusses her article appearing in the November 2011 issue of Mayo Clinic Proceedings that establishes a relationship between two genetic polymorphisms and the nutrophil count in patients who have experienced a heart attack. Available at: .

Demo: Variation for the ZAP70 gene with Ensembl

submitted by: gspudich

We use the Ensembl genome browser at to view small scale sequence variants such as SNPs (single nucleotide polymorphims) along with larger structural variations like CNVs (copy number variation) for the human ZAP70 gene.

Video tip of the week: Variation Data from Ensembl

submitted by: OpenHelix

For more information about this resource see our blog post at URL In today's tip I am going redo a movie originally done by Ensembl on SNP information in Ensembl, but I will use the updated Ensembl release 64.

Tip of the Week: VnD Resource for Genetic Variation and Drug Information

submitted by: OpenHelix

For more information about this resource, please see our blog post at URL In this tip I introduce users to the VnD, or genetic Variation and Drug database from the Korean Bioinformation Center, or KOBIC.

Michael Rhodes on "SOLiD Finishing - High Throughput Sequencing, Assembly and Analysis"

submitted by: JGI

Michael Rhodes of Applied Biosystems discusses the SOLiD System at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM on May 27, 2009.

Finding polymorphic Rat SNPs using RGD's SNPlotyper tool

submitted by: simont

This screencast shows how to identify polymorphic SNPs between different rat strains using RGD's SNPlotyper tool and the STAR consortium SNP genotype dataset. SNPlotyper is available at the Rat Genome Database ( and contains SNP genotype data produced by the european STAR consortium (