ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins

Bioinformatics. 2016 Aug 15;32(16):2499-501. doi: 10.1093/bioinformatics/btw068. Epub 2016 Apr 7.


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 App for Integrated Genome Browser, an open source desktop genome browser available from


MeSH terms

  • Alternative Splicing*
  • Genome*
  • Genomics
  • Humans
  • Molecular Sequence Annotation
  • Proteins
  • Web Browser


  • Proteins