title: ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.
abstract: 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.
  
  
  
  ProtAnnot is a plug-in App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org
  
  
  
  aloraine@uncc.edu.
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: Tarun
authors.initials: T
authors.lastname: Mall
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: John
authors.initials: J
authors.lastname: Eckstein
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: David
authors.initials: D
authors.lastname: Norris
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: Hiral
authors.initials: H
authors.lastname: Vora
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: Nowlan H
authors.initials: NH
authors.lastname: Freese
authors.affiliation: Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Kannapolis, NC 28081, USA.
authors.forename: Ann E
authors.initials: AE
authors.lastname: Loraine
mesh_terms: D017398:Alternative Splicing; D016678:Genome; D023281:Genomics; D006801:Humans; D058977:Molecular Sequence Annotation; D011506:Proteins; D064878:Web Browser
chemical_list: D011506:Proteins