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Analysis of Genomic Variations with AVIA

Annotation, Visualization, and Impact Analysis

We developed an interactive web-based tool, AVIA, to explore and interpret large sets of genomic variations (single nucleotide variations and small insertion/deletions) to help guide and summarize genomic experiments. The tool is based on coupling a comprehensive annotation pipeline with a flexible visualization method. We leveraged the ANNOVAR (Wang et. al, 2010) framework for assigning functional impact to genomic variations by extending its list of reference annotation databases (RefSeq, UCSC, SIFT, Polyphen etc.) with additional in-house developed sources (Non-B DB, PolyBrowse). Further, because many users also have their own annotation sources, we have added the ability to supply their own files as well.

The original version of AVIA is focused on gene related impact assessment; however, AVIAv2.0 extends its original implementation by adding information focusing on epigenetics, gene expression, and protein annotations. These data sources include Encode, NetPath, Uniprot, PharmGKB, GSEA, TargetScan, and many others. We have over 40 genomic databases and several new visualization options including use of jsmol for protein visualization, PathView-a KEGG map visualization tool, and Circos. Also, we have integrated several tools for prioritization.

During exploratory work with AVIA, users explore their data with the different databases, visualization and prioritization tools. Our most recent implementations strengthens AVIA as a comprehensive web-based resource that integrates annotation, visualization, and impact analysis.

If you already have mapped genomic data from human, please click here to get started.