The Human PAML Browser

Selection can be inferred through phylogenetic analysis by comparing the rates of silent and replacement substitution between related species. Maximum-likelihood (ML) analysis of codon substitution models can be used to identify genes with an accelerated pattern of amino acid substitution on a particular lineage. However, the ML methods are computationally intensive and awkward to configure. We have created a database that contains the results of tests for positive selection along the human lineage in 13,721 genes with orthologs in the UCSC multispecies genome alignments. The Human PAML Browser is a resource through which researchers can search for a gene of interest or groups of genes by Gene Ontology category, and obtain coding sequence alignments for the gene and as well as results from tests of positive selection from the software package Phylogenetic Analysis by Maximum Likelihood.通过比较近缘物种间的同义替换与非同义替换速率，可依托系统发育分析推断选择作用。基于密码子替换模型的最大似然（Maximum-likelihood, ML）分析，可用于鉴定特定谱系中氨基酸替换速率加快的基因。然而，ML方法计算复杂度高且配置流程繁琐。我们构建了一个数据库，收录了13721个在UCSC多物种基因组比对中存在直系同源基因的人类谱系正选择检测结果。人类PAML浏览器（Human PAML Browser）是一款科研资源，研究者可通过基因本体（Gene Ontology）类别检索目标基因或基因集，获取对应基因的编码序列比对结果，以及基于最大似然法系统发育分析软件包（Phylogenetic Analysis by Maximum Likelihood）得到的正选择检测结果。