ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.
ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins.
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DOI：
10.1093/bioinformatics/btw068
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发表时间：
2016-08-15
期刊：
影响因子：
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通讯作者：
Loraine AE
中科院分区：
文献类型：
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作者：
Mall T;Eckstein J;Norris D;Vora H;Freese NH;Loraine AE
一个基因可以产生多个转录变体，编码具有不同功能的蛋白质。为了便于对转录变体进行可视化分析，我们开发了ProtAnnot，它在基因组序列的背景下显示蛋白质注释。ProtAnnot搜索InterPro并显示与基因模型匹配的图谱（蛋白质注释），揭示替代启动子，剪接和3 '端加工如何添加，删除或重塑功能基序。为了引起人们对这些效应的注意，ProtAnnot对外显子按帧进行颜色编码，并显示一个城市景观图形，总结每个位置的外显子序列。这些技术使生物学家更快、更方便地对替代转录本进行可视化分析。可用性和实施：ProtAnnot是一个插件应用程序集成基因组浏览器，一个开源的桌面基因组浏览器可从http://www.bioviz.org.联系：aloraine@uncc.edu
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