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About

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Analysis of Genomic Variations with AVIA
About AVIA

AVIA is a web based annotation and visualization workflow that allow users with variation data to easily get more information about their specific mutations without having to search multiple websites or databases. Below is a brief description of the features of AVIA. Please view our comparison chart here.
  • INPUT
    • variation data mapped to human genome in genomic coordinates
  • OUTPUT(S) Click here to view sample results.
    • Table of annotations with gene annotation features
      • Complete list of annotation database found here
      • Prioritized gene list based on categories affecting gene regulation or protein
      • Uniprot annotations for features such as domains, protein-protein interactions, disease, etc with link out
      • Intgration of DAVID API with link out to DAVID, gene enrichment pathways
      • Link out to GeneMania, a web based cytoscape plugin
      • Prioritization of variants using FunSeq workflow
      • Normal Gene Expression prioritization using GNF data and API
    • Visualization By Input
      • Circos representation of the raw data and annotated data
      • jmol representation of in-house built protein structures to show regions of amino acid changes
      • Summary plots of the data
      • If specified, KEGG pathway graphs rendered with PathView with state data
Interactive Features available on the website

  • Filtering of data set
  • Regeneration of multi-tiered Circos plots
  • Annotation of custom databases
  • Link outs for more information on specific mutations
  • BioGPS API for Normal tissue expression
  • Exploratory database search by gene
  • jsmol for a subset of modelled proteins
  • Search capabilities within dataset
Major Differences between other web-based annotations programs

  • Comprehensive set of genomic annotation databases (>40 databases)
  • Focus on non-coding regions as well as coding
  • Easily adds additional user databases
  • Predictions for non-coding miRNA folding
  • Prioritization of variants by Summary Codes and prioritized gene list

All user data readily available for download. Databases are obtained from publicly available sources.