Kuang Zheng, Canzar Stefan
Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
Methods Mol Biol. 2018;1751:73-88. doi: 10.1007/978-1-4939-7710-9_5.
Alternative splicing increases the functional complexity of a genome by generating multiple isoforms and potentially proteins from the same gene. Vast amounts of alternative splicing events are routinely detected by short read deep sequencing technologies but their functional interpretation is hampered by an uncertain transcript context. Emerging long-read sequencing technologies provide a more complete picture of full-length transcript sequences. We introduce SpliceHunter, a tool for the computational interpretation of long reads generated by for example Pacific Biosciences instruments. SpliceHunter defines and tracks isoforms and novel transcription units across time points, compares their splicing pattern to a reference annotation, and translates them into potential protein sequences.
可变剪接通过从同一基因产生多种异构体甚至潜在的蛋白质，增加了基因组的功能复杂性。短读长深度测序技术常规检测到大量可变剪接事件，但其功能解释因转录本背景不确定而受到阻碍。新兴的长读长测序技术能提供更完整的全长转录本序列信息。我们引入了SpliceHunter，这是一种用于对例如由太平洋生物科学公司仪器生成的长读长进行计算解释的工具。SpliceHunter可定义并跟踪不同时间点的异构体和新转录单元，将其剪接模式与参考注释进行比较，并将它们翻译成潜在的蛋白质序列。
