28-way vertebrate alignment and conservation track in the UCSC Genome Browser
28-way vertebrate alignment and conservation track in the UCSC Genome Browser
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DOI：
10.1101/gr.6761107
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发表时间：
2007-12-01
期刊：
影响因子：
7
通讯作者：
Kent, W. James
中科院分区：
文献类型：
--
作者：
Miller, Webb;Rosenbloom, Kate;Kent, W. James
这篇文章描述了一组由UCSC基因组浏览器提供的28个脊椎动物基因组序列的比对。比对结果可以在http://genome.ucsc.eduhttp://hgdownload.cse.ucsc.edu/goldenPath/组装）上查看，通过匿名FTP从www.example.comhg 18/multiz 28 way批量下载，或在http://g2.bx.psu.edu用Galaxy服务器分析。本文通过三个例子说明了这种资源在探索脊椎动物和哺乳动物进化方面的力量。首先，我们介绍了几个涉及蛋白质编码区内插入和缺失的小插曲，包括一些人类特异性indel。然后，我们研究了在人类序列中的起始密码子和终止密码子在其他物种中保守的程度，表明起始密码子通常比终止密码子保守得更差。最后，对人类基因组中几类功能元件的系统发育保守深度的调查揭示了可重复性衰减的速率和模式的显著差异。每个功能类别都有一个独特的严格约束期，然后是允许（对于调节区的情况）或拒绝（对于编码区和超保守元件）插入和缺失的衰变。
This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser ( March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/ hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow ( for the case of regulatory regions) or reject ( for coding regions and ultraconserved elements) insertions and deletions.