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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.


This is a two-part workshop. Part-1, the morning session provides a brief overview of human genetic variations with the introduction to various genetic variation databases (dbSNP, ClinVar, HGMD, COSMIC, TumorPortal, gnomAD, and RegulomeDb). 

Part-2, the afternoon session  covers variant identification using the HSLS-licensed software CLC Genomics Workbench, how to use bioinformatics tools for functional analysis of mutations, and open-access web tools such as Ensembl Variant Effect Predictor and wANNOVAR

Target Audience

Experimental biologists seeking to identify genetic variations from Whole Exome or Whole Genome Sequencing data. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command line interface is required.

Workshop Materials


  • Slides
  • Practice Exercise

Data Download

Pre-analyzed Results

Tutorials and Documentations


  • Knoweng - An interactive learning resource for next-generation sequencing (NGS) techniques

Databases and Tools


  • Human Gene Mutation Database 
  • dbSNP - contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
  • 1000 Genomes - a catalogue of common human genetic variation,
  • dbVAR - NCBI's database of human genomic Structural Variation
  • EBI GWAS Catalog - Catalog of human genome-wide association studies
  • Decipher - used by the clinical community to share and compare phenotypic and genotypic data.
  • NCBI PheGenI - he Phenotype-Genotype Integrator (PheGenI), merges NHGRI genome-wide association study (GWAS) catalog data with several databases housed at the National Center for Biotechnology Information (NCBI), including Gene, dbGaP, OMIM, eQTL and dbSNP. 
  • ClinVar - aggregates information about genomic variation and its relationship to human health.
  • PharmGKB - Pharmacogenomics knowledge for personalized medicine
  • Cosmic - the Catalogue Of Somatic Mutations In Cancer,
  • Tumor Portal - provides Genes, Cancers, DNA Mutations & Annotations
  • OMIM-a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily
  • GnomAD Browser - genome aggregation database

Functional Analysis Tools

  • Entrez SNP - search engine for dbSNP
  • Entrez Protein  - search NCBI protein database
  • TMHMM Server - Prediction of transmembrane helices in proteins
  • ESE Finder
  • Variant Effect Predictor- a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data
  • wANNOVAR- a rapid, efficient tool to annotate functional consequences of genetic variation from high-throughput sequencing data.
  • PredictSNP2 - a platform for prediction of SNP effect

Feedback & Support


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