Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately — or cannot be annotated at all — by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements — not included in the ground truth — revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs — with its speed, accuracy, and novel features — represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.

中文翻译：

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Look4LTRs：一种长末端重复逆转录转座子检测工具，能够进行跨物种研究并发现最近嵌套的重复

植物基因组包含大量转座元件。这些元件的一种特殊类型两侧是两个长末端重复序列 (LTR)，并且可以使用 RNA 进行易位。这些元件被称为LTR-逆转录转座子；它们是植物基因组中最丰富的转座子类型。它们具有许多重要的功能，包括基因调控以及新基因和假基因的出现以应对严重压力。此外，LTR-逆转录转座子在生物技术中有多种应用。由于 LTR 反转录转座子的丰富性和重要性，已经开发了多种计算工具用于其检测。然而，这些工具都没有利用相关基因组的可用性。它们一次处理一条染色体。此外，当前可用的工具无法准确注释或根本无法注释最近嵌套的 LTR 逆转录转座子（同一家族的多个元件相互插入）。为了克服这两个限制，我们构建了 Look4LTR，它可以同时注释多个相关基因组中的 LTR 逆转录转座子并发现最近嵌套的元素。 Look4LTR 的方法取决于从信号处理领域引入的技术、图形算法和机器学习，并最少使用对齐算法。四种植物基因组用于开发 Look4LTR，八种植物基因组用于与三种相关工具进行对比评估。 Look4LTR 是最快的，同时保持与其他工具获得的更好或相当的 F1 分数（召回率和精确率的调和平均值）。我们的结果证明了同时注释多个相关基因组中的 LTR 逆转录转座子的额外好处以及发现最近嵌套元素的能力。专家对六种元素（未包含在基本事实中）的人工检查显示，三种元素属于已知家族，两种元素可能来自新家族。关于检查最近嵌套的 LTR 反转录转座子，五分之三被确认为有效元件。 Look4LTR 以其速度、准确性和新颖的特点，代表了 LTR 反转录转座子注释的真正进步，为许多专注于了解其在植物中功能的研究打开了大门。