ProtAnnot: Visualizing Protein Function and Effects of Alternative Transcription

ProtAnnot is a new optional plug-in App for the Integrated Genome Browser (IGB) that displays protein annotations in the context of genomic sequence.  To run ProtAnnot, users select one or more gene models in IGB and choose Tools > Open ProtAnnot. This opens ProtAnnot in a separate window, showing a new view of the selected gene models. In ProtAnnot, exons are color-coded by the frame of translation, making it easy to notice when splicing differences cause frameshifts in the gene models. Below the gene models is an exon summary graphic, where differences in block heights indicate difference regions, segments of genomic sequence that are included in one gene model and not the other. To identify regions within gene models likely to be important for gene function, users can search the InterPro database from within ProtAnnot. To run a search, users select “Run InterProScan”. This opens a menu with options to select and then search any of the sixteen profile databases available from InterPro. Once the search completes, protein annotations are mapped onto the genomic sequence alongside gene models. Selecting protein annotations displays more information, including name, description and links to more information. Viewing and interacting with protein annotations displayed in ProtAnnot helps with identifying conserved domains within a protein and overall gene function. An easy-to-use Image Export tool generates high-resolution ProtAnnot images for use in printed publications or slide presentations. ProtAnnot and IGB are freely available from http://www.bioviz.org.