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SCOPE plus plus : Sequence Classification Of homoPolymer Emissions

机译：SCOPE plus plus：均聚物发射的序列分类

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Background: mRNA polyadenylation, the addition of a poly(A) tail to the 3'-end of pre-mRNA, is a process critical to gene expression and regulation in eukaryotes. To understand the molecular mechanisms governing polyadenylation and other relevant biological processes, it is important to identify these poly(A) tails accurately in transcriptome sequencing data and differentiate them from artificial adapter sequences added in the sequencing process. But the annotation of these tails is complicated by the presence of sequencing errors and post-transcriptional modifications. While determining that a tail is present in a given transcript fragment is straight-forward, these obfuscations make the problem of boundary identification a challenge; conventional seed-and-extend algorithms struggle to accurately identify these poly(A) tail end-points. Further, all existing tools that we are aware of focus exclusively on the trimming of poly(A) tails, failing to provide the detailed information needed for studying the polyadenylation process.
机译：背景：mRNA聚腺苷酸化是在pre-mRNA的3'末端添加一个poly（A）尾部，是真核生物中基因表达和调控的关键过程。要了解控制聚腺苷酸化和其他相关生物学过程的分子机制，重要的是在转录组测序数据中准确鉴定出这些poly（A）尾巴，并将它们与测序过程中添加的人工衔接子序列区分开。但是由于测序错误和转录后修饰的存在，这些尾巴的注释变得复杂。虽然确定给定的转录片段中存在尾巴是直接的，但这些混淆使边界识别的问题成为一个挑战。传统的种子扩展算法难以准确地识别这些poly（A）尾点。此外，我们知道的所有现有工具都只专注于修剪poly（A）尾部，未能提供研究聚腺苷酸化过程所需的详细信息。

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