Team IOBIO releases gene.iobio

The Marth laboratory at the USTAR Center for Genetic Discovery has created gene.iobio, a genomics software tool for real-time analysis of disease-causing genetic variants over the web.

Gene.iobio is geared toward clinicians and researchers who’d like to query their genomic data but have limited bioinformatics expertise and equipment. The app integrates multiple tools and data sources into a single user-friendly web interface. Users can analyze their variants and alignments in one place without uploading files. No command line or data tables – outputs are displayed visually using a series of elegant graphical representations. A laptop and internet connection are the only requirements.

The tool supports variant prioritization, annotation of variants with snpEff to predict functional effect, calculation of base coverage, and assignment of inheritance patterns for trios. The application also pulls in data from 1000 Genomes and ExAC to calculate allele frequencies, and from ClinVar to calculate pathogenicity and phenotype associated with a particular variant. The user can select from a list of transcripts and perform analyses on any alternative gene model. Variants can be called in real-time with Freebayes, identifying new variants not present in the original dataset.

The gene.iobio app is new and Team IOBIO requests your feedback! Try it here on your own dataset or use our sample datasets. Send your questions and feedback to iobioproject@gmail.com.   Discuss your gene.iobio experience here, or on the Biostars.org forum using the tag #iobio.

Lead developers for gene.iobio are Tonya Di Sera, Chase Miller, Yi Qiao, and Alistair Ward from the Marth Laboratory at the USTAR Center for Genetic Discovery at University of Utah. This work is supported by the National Human Genome Research Institute (NHGRI) and by the Utah Science, Technology and Research (USTAR) initiative

Tonya Di Sera, Lead Developer for gene.iobio