How to usefully compare homologous plant genes and chromosomes as DNA sequences
How to usefully compare homologous plant genes and chromosomes as DNA sequences
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DOI：
10.1111/j.1365-313x.2007.03326.x
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发表时间：
2008-02-01
期刊：
影响因子：
7.2
通讯作者：
Freeling, Michael
中科院分区：
文献类型：
--
作者：
Lyons, Eric;Freeling, Michael
迄今为止，有四种已测序且公开的植物基因组。随着更多的工作即将完成，一项挑战将是使用比较基因组方法来检测植物基因组中的新进化模式。这项研究需要序列比对算法来检测基因组内部和基因组之间的相似区域。然而，不同的比对算法针对识别不同类型的同源序列进行了优化。这篇综述重点关注植物基因组进化，并提供了使用几种序列比对算法和可视化工具来检测有用的保守模式的教程：保守的非编码序列、假阳性噪声、亚功能化、同线性、注释错误、倒位和局部重复。我们的教程鼓励读者使用经过审查的工具在线进行实验，作为文本的补充。
There are four sequenced and publicly available plant genomes to date. With many more slated for completion, one challenge will be to use comparative genomic methods to detect novel evolutionary patterns in plant genomes. This research requires sequence alignment algorithms to detect regions of similarity within and among genomes. However, different alignment algorithms are optimized for identifying different types of homologous sequences. This review focuses on plant genome evolution and provides a tutorial for using several sequence alignment algorithms and visualization tools to detect useful patterns of conservation: conserved non-coding sequences, false positive noise, subfunctionalization, synteny, annotation errors, inversions and local duplications. Our tutorial encourages the reader to experiment online with the reviewed tools as a companion to the text.