利用基因和物种树的系统发育比较鉴定G蛋白偶联受体亚家族
G-protein coupled receptor subfamily identification using phylogenetic comparison of gene and species trees
摘要：
大多数从蛋白质初生结构预测蛋白质功能的方法是基于查询序列与已知功能序列之间的相似性。然而，这种方法忽略了基因复制（旁系）或基因的趋同进化的发生。考虑到所研究基因的进化历史，对共享共同结构域的相关蛋白质的分析可以为具有未知功能的预测蛋白质提供更可靠的注释。开发了一个计算机程序，可以实时比较“基因树”与“物种树”。系统发生基因组注释器（PGA）对共享共同结构域的一组序列进行基于谱的多个序列比对，以生成系统发生基因树，将其与从比对的核糖体RNA数据推断的物种系统发生进行比较。然后，相关的蛋白质结构域与相应物种的同源性并排显示。用四重困惑法给出了基因簇（分支）的统计支持。这种分析很容易区分旁系同源物和直系同源物，从而能够鉴定由基因重复产生的蛋白质，并预测相似序列组中可能的功能差异。该工具在G蛋白偶联受体超家族的三个不同的亚家族中进行了测试。在分析的数据集，旁系预测同意与已知的亚科分组，这表明亚科分歧是由祖先节点的重复事件。
英文摘要：
Most approaches to prediction of protein function from primary structure are based on similarity between the query sequence and sequences of known function. This approach, however, disregards the occurrence of gene duplication (paralogy) or convergent evolution of the genes. The analysis of correlated proteins that share a common domain, taking into consideration the evolutionary history of genes under study may provide a more reliable annotation of predicted proteins with unknown function. A computer program that enables real-time comparison of 'gene trees' with 'species trees' was developed. The Phylogenetic Genome Annotator (PGA) performs a profile based multiple sequence alignment of a set of sequences that share a common domain to generate a phylogenetic gene tree, which is compared to the species phylogeny inferred from aligned ribossomal RNA data. The correlated protein domains are then displayed side-by-side with the phylogeny of the corresponding species. The statistical support of gene clusters (branches) is given by the quartet puzzling method. This analysis readily discriminates paralogs from orthologs, enabling the identification of proteins originated by gene duplications and the prediction of possible functional divergence in groups of similar sequences. The tool was tested in three distinct subfamilies of the G-protein coupled receptor superfamily. In the analysed datasets, the paralogy prediction agreed with the known subfamily grouping, suggesting that subfamily divergence was facilitated by duplication events in the ancestral nodes.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
