ProtAnnot: visualizing effects of alternative splicing and transcription on protein sequence and function in a genome browser

Summary: One gene can produce multiple transcript variants encoding proteins with different functions. To facilitate visual analysis of transcript variants, we developed ProtAnnot, which shows protein annotations in the context of genomic sequence. ProtAnnot searches InterPro and displays profile matches (protein annotations) alongside gene models, exposing how alternative promoters, splicing, and 3' end processing add, remove, or remodel functional motifs. To draw attention to these effects, ProtAnnot color-codes exons by frame and displays a cityscape graphic summarizing exonic sequence at each position. These techniques make visual analysis of alternative transcripts faster and more convenient for biologists. Availability and Implementation: ProtAnnot is a plug-in for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org. Videos showing ProtAnnot in action are available at http://bit.ly/igbchannel.