To effectively analyze the increasing amounts of available genomic data, improved comparative analytical tools that are accessible to and applicable by a broad scientific community are essential. We built the “2-n-way” software suite to provide a fundamental and innovative processing framework for revealing and comparing inserted elements among various genomes. The suite comprises two user-friendly web-based modules. The 2-way module generates pairwise whole-genome alignments of target and query species. The resulting genome coordinates of blocks (matching sequences) and gaps (missing sequences) from multiple 2-ways are then transferred to the n-way module and sorted into projects, in which user-defined coordinates from reference species are projected to the block/gap coordinates of orthologous loci in query species to provide comparative information about presence (blocks) or absence (gaps) patterns of targeted elements over many entire genomes and phylogroups. Thus, the 2-n-way software suite is ideal for performing multidirectional, non-ascertainment-biased screenings to extract all possible presence/absence data of user-relevant elements in orthologous sequences. To highlight its applicability and versatility, we used 2-n-way to expose approximately 100 lost introns in vertebrates, analyzed thousands of potential phylogenetically informative bat and whale retrotransposons, and novel human exons as well as thousands of human polymorphic retrotransposons.

中文翻译：

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多比较 2-n-way 基因组套件。

为了有效地分析越来越多的可用基因组数据，广泛的科学界可以使用和适用的改进的比较分析工具是必不可少的。我们构建了“2-n-way”软件套件，为揭示和比较各种基因组之间的插入元素提供了一个基本的和创新的处理框架。该套件包括两个用户友好的基于 Web 的模块。2-way 模块生成目标物种和查询物种的成对全基因组比对。然后将来自多个 2-way 的块（匹配序列）和间隙（缺失序列）的基因组坐标转移到 n-way 模块并分类到项目中，其中来自参考物种的用户定义坐标被投影到查询物种中直系同源基因座的块/间隙坐标，以提供有关目标元素在许多整个基因组和系统群中存在（块）或不存在（间隙）模式的比较信息。因此，2-n-way 软件套件非常适合执行多向、非确定性偏见筛选，以提取直系同源序列中用户相关元素的所有可能存在/不存在数据。为了突出其适用性和多功能性，我们使用 2-n-way 暴露了脊椎动物中大约 100 个丢失的内含子，分析了数千个潜在的系统发育信息蝙蝠和鲸鱼逆转录转座子，以及新的人类外显子以及数千个人类多态性逆转录转座子。