Human Genetics

, Volume 132, Issue 11, pp 1235–1243 | Cite as

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures

  • Noushin Niknafs
  • Dewey Kim
  • RyangGuk Kim
  • Mark Diekhans
  • Michael Ryan
  • Peter D. Stenson
  • David N. Cooper
  • Rachel Karchin
Original Investigation

Abstract

Mutation position imaging toolbox (MuPIT) interactive is a browser-based application for single-nucleotide variants (SNVs), which automatically maps the genomic coordinates of SNVs onto the coordinates of available three-dimensional (3D) protein structures. The application is designed for interactive browser-based visualization of the putative functional relevance of SNVs by biologists who are not necessarily experts either in bioinformatics or protein structure. Users may submit batches of several thousand SNVs and review all protein structures that cover the SNVs, including available functional annotations such as binding sites, mutagenesis experiments, and common polymorphisms. Multiple SNVs may be mapped onto each structure, enabling 3D visualization of SNV clusters and their relationship to functionally annotated positions. We illustrate the utility of MuPIT interactive in rationalizing the impact of selected polymorphisms in the PharmGKB database, somatic mutations identified in the Cancer Genome Atlas study of invasive breast carcinomas, and rare variants identified in the exome sequencing project. MuPIT interactive is freely available for non-profit use at http://mupit.icm.jhu.edu.

Supplementary material

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Supplementary material 1 (PNG 227 kb)
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Supplementary material 2 (PNG 213 kb)
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Supplementary material 3 (PNG 140 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Noushin Niknafs
    • 1
  • Dewey Kim
    • 1
  • RyangGuk Kim
    • 2
  • Mark Diekhans
    • 3
  • Michael Ryan
    • 2
  • Peter D. Stenson
    • 4
  • David N. Cooper
    • 4
  • Rachel Karchin
    • 1
  1. 1.Department of Biomedical Engineering, Institute for Computational MedicineJohns Hopkins UniversityBaltimoreUSA
  2. 2.In Silico SolutionsFairfaxUSA
  3. 3.Center for Biological Science and EngineeringUniversity of CaliforniaSanta CruzUSA
  4. 4.Institute of Medical Genetics, School of MedicineCardiff UniversityCardiffUK

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