Software and Services

We develop and maintain a variety of software and web services.

Tools for Assessment of Variants

  • PolyPhen-2 is a tool for predicting the effect of an amino acid substitution on protein structure and function, based on comparative genomics and experimentally determined protein structures. It is available as a web service, and can also be downloaded as a standalone application.
  • SNPtrack is a simple interface for mutation mapping and identifying causal mutations from whole-genome sequencing studies. It is available as a web service.
  • SCONE is a tool for predicting the effect of noncoding variation on regulatory sequences based on evolutionary conservation. It is available for download as a standalone application.
  • PINES (Phenotype-Informed Noncoding Element Scoring) evaluates the functional impact of noncoding variants by integrating diverse epigenetic annotations, utilizing genomic annotations most relevant to phenotypes of interest.

Tools for Mass Spectrometry and Proteomics

  • EagleEye is a tool for filtering noise and background proteins from LC-MS/MS spectra. It is available as a web service.
  • MS-BLAST is a tool for searching protein sequences identified with tandem mass spectrometry against databases of protein sequences. It is available as a web service.

Tools for Statistical Genetics

  • Joint Likelihood Mapping (JLIM) is a tool to test for shared genetic effect between two genetic association data, for example, a disease GWAS study and gene expression QTL (eQTL) study.
  • Joint Likelihood Mapping 2 (JLIM_2.0) is a version of JLIM which supports meta-analysis across more than one cohort of matching ancestry.
  • NPS is a tool for polygenic risk scoring based on partitioning-based non-parametric shrinkage algorithm.

Tools for Cancer Genomics

  • CBaSE enables cancer type and gene-specific estimation of the strength of negative and positive selection. It is available as a browser-based tool as well as for download as a standalone package.