PT  - JOURNAL ARTICLE
AU  - Tarun Mall
AU  - John Eckstein
AU  - David Norris
AU  - Hiral Vora
AU  - Nowlan Freese
AU  - Ann E. Loraine
TI  - ProtAnnot: visualizing effects of alternative splicing and transcription on protein sequence and function in a genome browser
AID  - 10.1101/025924
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 025924
4099  - http://biorxiv.org/content/early/2015/09/11/025924.short
4100  - http://biorxiv.org/content/early/2015/09/11/025924.full
AB  - 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.Contact aloraine{at}uncc.edu