Functional Annotation of Custom Transcriptomes.
Functional Annotation of Custom Transcriptomes.
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自定义转录组的功能注释。
DOI：
10.1007/978-1-0716-2521-7_9
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发表时间：
2022
期刊：
影响因子：
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通讯作者：
Hamid F
中科院分区：
文献类型：
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作者：
Hamid F
许多真核基因可以根据发育阶段、细胞类型和生理线索产生不同的替代转录本。当前的全转录组测序技术突出了后生动物中这种调节的显著程度，并允许在越来越小的生物样本中分析RNA同工型，并且越来越有信心。了解样本特异性转录物的生物学功能是基因组学和RNA加工领域的主要挑战。在这里，我们描述了简单的生物信息学工作流程，通过简化参考指导的新转录物注释来促进这项任务。我们的方案的一个关键部分是R包因子，它可以快速匹配定制组装的转录本与其可能的宿主基因，推断新蛋白产物的序列和结构域结构，并预测新鉴定的RNA异构体对无义介导的衰变的敏感性。
Many eukaryotic genes can give rise to different alternative transcripts depending on stage of development, cell type, and physiological cues. Current transcriptome-wide sequencing technologies highlight the remarkable extent of this regulation in metazoans and allow for RNA isoforms to be profiled in increasingly small biological samples and with a growing confidence. Understanding biological functions of sample-specific transcripts is a major challenge in genomics and RNA processing fields. Here we describe simple bioinformatics workflows that facilitate this task by streamlining reference-guided annotation of novel transcripts. A key part of our protocol is the R packagefactRthat rapidly matches custom-assembled transcripts to their likely host genes, deduces the sequence and domain structure of novel protein products, and predicts sensitivity of newly identified RNA isoforms to nonsense-mediated decay.