QuartetS: a fast and accurate algorithm for large-scale orthology detection.
QuartetS: a fast and accurate algorithm for large-scale orthology detection.
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DOI：
10.1093/nar/gkr308
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发表时间：
2011-07
影响因子：
14.9
通讯作者：
Reifman J
中科院分区：
文献类型：
--
作者：
Yu C;Zavaljevski N;Desai V;Reifman J
基因组数据可用性的空前增长既对开发同时准确和高通量的同源检测方法提出了挑战，也为利用积累的测序基因组中的进化证据来改进同源检测提供了机会。在这里，我们报告了一种新的形态学检测方法，称为四重奏，利用进化证据在计算有效的方式。基于基因重复事件可以用来区分同源基因这一成熟的进化概念，QuartetS利用对四重奏基因树的近似系统发育分析来推断重复事件的发生并区分同源基因和同源基因。我们使用基于功能和系统发育的指标对QuartetS与其他四种方法[双向最佳命中（BBH），外群，OMA和QuartetS- c（四重奏跟随聚类）]的同源预测进行了大规模，系统的比较，涉及624个细菌基因组和bb220万个基因。我们发现QuartetS略微优于高度特异性的OMA方法，虽然只消耗0.5%的额外计算时间，但与广泛使用的BBH方法相比，QuartetS预测的同源物多50%，假阳性率低50%。我们得出结论，对于大规模的系统发育和功能分析，在需要高精度和高通量的应用中，QuartetS和QuartetS- c应该分别是首选。
The unparalleled growth in the availability of genomic data offers both a challenge to develop orthology detection methods that are simultaneously accurate and high throughput and an opportunity to improve orthology detection by leveraging evolutionary evidence in the accumulated sequenced genomes. Here, we report a novel orthology detection method, termed QuartetS, that exploits evolutionary evidence in a computationally efficient manner. Based on the well-established evolutionary concept that gene duplication events can be used to discriminate homologous genes, QuartetS uses an approximate phylogenetic analysis of quartet gene trees to infer the occurrence of duplication events and discriminate paralogous from orthologous genes. We used function- and phylogeny-based metrics to perform a large-scale, systematic comparison of the orthology predictions of QuartetS with those of four other methods [bi-directional best hit (BBH), outgroup, OMA and QuartetS-C (QuartetS followed by clustering)], involving 624 bacterial genomes and >2 million genes. We found that QuartetS slightly, but consistently, outperformed the highly specific OMA method and that, while consuming only 0.5% additional computational time, QuartetS predicted 50% more orthologs with a 50% lower false positive rate than the widely used BBH method. We conclude that, for large-scale phylogenetic and functional analysis, QuartetS and QuartetS-C should be preferred, respectively, in applications where high accuracy and high throughput are required.
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影响因子：
4.3
作者：
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通讯作者：
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通讯作者：
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