Cactus: Algorithms for genome multiple sequence alignment
Cactus: Algorithms for genome multiple sequence alignment
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DOI：
10.1101/gr.123356.111
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发表时间：
2011-09-01
期刊：
影响因子：
7
通讯作者：
Haussler, David
中科院分区：
文献类型：
--
作者：
Paten, Benedict;Earl, Dent;Haussler, David
在包含取代、插入和缺失的模型中创建可靠的多序列比对的问题已经引起了很多关注。在更普遍的重排和拷贝数变异的存在下，对优化比对的问题关注得少得多。使用仙人掌图，最近推出的代表序列比对，我们描述了两个互补的算法，用于创建基因组比对。我们已经在新的“仙人掌”比对程序中实现了这些算法。我们测试仙人掌使用进化基因组进化模拟器，一个全面的新的模拟工具，并显示使用这些和现有的模拟，仙人掌显着优于所有的同行。最后，我们对仙人掌正确排列基因的能力进行了实证评估，并在灵长类动物中发现了有趣的基因内重复的情况。
Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new "Cactus'' alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactus's ability to properly align genes and find interesting cases of intra-gene duplication within the primates.