MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement.
MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement.
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DOI：
10.1186/1471-2105-11-10
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发表时间：
2010-01-06
影响因子：
3
通讯作者：
Jiang T
中科院分区：
文献类型：
--
作者：
Shi G;Zhang L;Jiang T
直系分配是比较基因组学的关键和基本问题，因为直系同源物被认为是不同物种的功能性对应物，可用于从其他物种的物种中推断出一种物种的分子功能。 MSOAR是一种最近开发的高通量系统，用于在基因组量表上分配紧密相关的物种之间的一对一直系同源物。它试图根据基因组重排和基因复制事件来重建输入基因组的进化史。它假设基因重复事件将重复的基因插入随机位置的感兴趣基因组（即随机重复模型）。但是，实际上，生物学家认为基因通常是通过串联重复来复制的，其中重复的基因位于原始副本旁边（即串联重复模型）。
在本文中，我们开发了MSOAR 2.0，这是一种改进的系统，用于一对一的直系同源分配。对于一对输入基因组，该系统首先着重于每个基因组的串联重复基因，并尝试使用简单的系统生理树对核方法来识别物种后重复的人（即所谓的非子代表）。对于每一套这样的串联复制的子谱系，除一个基因以外的所有基因都将从相关的基因组中删除（因为它们不可能出现在任何一对一的直系同源对中），并调用了MSOAR。使用模拟和实际数据实验，我们表明MSOAR 2.0能够比MSOAR获得更好的灵敏度和特异性。与众所周知的基因组规模的直系同源分配工具Inparanoid，Ensembl Ortholog Database以及从众所周知的全基因组多元对齐程序Multiz中提取的矫正信息MSOAR 2.0显示出最高的灵敏度。尽管在实际数据实验中，MSOAR 2.0的特异性比非paranoid的特异性稍差，但在仿真测试中，它实际上比异烷类的特异性要好。
我们的初步实验结果表明，MSOAR 2.0是在紧密相关的基因组之间一对一直系分配的高度精确工具。该软件免费提供给公众，并作为在线补充材料。
Ortholog assignment is a critical and fundamental problem in comparative genomics, since orthologs are considered to be functional counterparts in different species and can be used to infer molecular functions of one species from those of other species. MSOAR is a recently developed high-throughput system for assigning one-to-one orthologs between closely related species on a genome scale. It attempts to reconstruct the evolutionary history of input genomes in terms of genome rearrangement and gene duplication events. It assumes that a gene duplication event inserts a duplicated gene into the genome of interest at a random location (i.e., the random duplication model). However, in practice, biologists believe that genes are often duplicated by tandem duplications, where a duplicated gene is located next to the original copy (i.e., the tandem duplication model). In this paper, we develop MSOAR 2.0, an improved system for one-to-one ortholog assignment. For a pair of input genomes, the system first focuses on the tandemly duplicated genes of each genome and tries to identify among them those that were duplicated after the speciation (i.e., the so-called inparalogs), using a simple phylogenetic tree reconciliation method. For each such set of tandemly duplicated inparalogs, all but one gene will be deleted from the concerned genome (because they cannot possibly appear in any one-to-one ortholog pairs), and MSOAR is invoked. Using both simulated and real data experiments, we show that MSOAR 2.0 is able to achieve a better sensitivity and specificity than MSOAR. In comparison with the well-known genome-scale ortholog assignment tool InParanoid, Ensembl ortholog database, and the orthology information extracted from the well-known whole-genome multiple alignment program MultiZ, MSOAR 2.0 shows the highest sensitivity. Although the specificity of MSOAR 2.0 is slightly worse than that of InParanoid in the real data experiments, it is actually better than that of InParanoid in the simulation tests. Our preliminary experimental results demonstrate that MSOAR 2.0 is a highly accurate tool for one-to-one ortholog assignment between closely related genomes. The software is available to the public for free and included as online supplementary material.
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DOI：
10.1073/pnas.0501102102
发表时间：
2005-04-12
影响因子：
11.1
作者：
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DOI：
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影响因子：
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DOI：
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发表时间：
1970-01-01
期刊：
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影响因子：
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作者：
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影响因子：
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作者：
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DOI：
10.1109/tcbb.2005.48
发表时间：
2005-10-01
影响因子：
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作者：
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