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

Tarun Mall,Nowlan H Freese,Hiral Vora,Ann E Loraine,David Norris,John Eckstein

doi:10.1093/bioinformatics/btw068

Tarun Mall, Nowlan H Freese + Show 4 more

Open Access

https://doi.org/10.1093/bioinformatics/btw068

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Abstract

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 App for Integrated Genome Browser, an open source desktop genome browser available from http://www.bioviz.org.Contact: aloraine@uncc.edu

Highlights

Many genes produce multiple transcript variants due to alternative splicing, alternative promoters, and alternative 3’ end processing
We developed ProtAnnot as a new plug-in extension for the Integrated Genome Browser (IGB)
ProtAnnot introduces an exon summary graphic, a series of blocks at the bottom of the display whose heights indicate the number of exons overlapping each position

Summary

Introduction

Many genes produce multiple transcript variants due to alternative splicing, alternative promoters, and alternative 3’ end processing. Often these transcript variants encode proteins with different amino acid sequences and different functions. Using Web tools (Rodriguez, et al, 2015), biologists can identify conserved regions in proteins encoded by different splice variants, but mapping those regions back onto gene structures is time-consuming and error-prone.

Results

Conclusion