Tertiary windowing to detect positive diversifying selection
Tertiary windowing to detect positive diversifying selection
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DOI：
10.1007/s00239-004-0223-4
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发表时间：
2005-04-01
影响因子：
3.9
通讯作者：
Liberles, DA
中科院分区：
文献类型：
--
作者：
Berglund, AC;Wallner, B;Liberles, DA
随着蛋白质编码基因的进化，不同的选择压力在时间和空间上作用于基因。对非同义核苷酸取代率比率（K-a/K-s）的检查已被证明是一种有价值的方法来检查蛋白质编码基因的选择压力，包括检测积极的多样化选择。为了获得平均一个基因中所有位点的能力，经常采用对初级序列窗口中的位点的检查。然而，选择作用于折叠的蛋白质和在三级空间中接近的位点可能在一级序列中不接近。介绍了一种基于三级结构窗口的K-a/K-s比值检测新方法，并将其应用于哺乳动物瘦素基因家族。三级序列窗口检测正向多样化选择下的新位点，并在瘦素基因家族树的各个分支上以更显著的信号检测正向多样化选择。
As a protein-encoding gene evolves, different selective pressures act on the gene temporally and spatially. An examination of the ratio of nonsynonymous-to-synonymous nucleotide substitution rate ratios (K-a/K-s) has proven to be a valuable method to examine selective pressures on protein encoding genes, including detecting positive diversifying selection. To gain power over averaging all sites in a gene together, examination of sites in primary sequence windows has frequently been employed. However, selection acts on folded proteins and sites that are close in tertiary space may not be close in primary sequence. A new method for the examination of K-a/K-s ratios based upon windows in tertiary structure is introduced and applied to the leptin gene family in mammals. Tertiary sequence windowing detects new sites under positive diversifying selection and detects positive diversifying selection with a more significant signal along various branches of the leptin gene family tree.