GeneSeqToFamily: Data

Gene duplication is a major factor contributing to evolutionary novelty, and the contraction or expansion of gene families has often been associated with morphological, physiological and environmental adaptations. The study of homologous genes helps us to understand the evolution of gene families. It plays a vital role in finding ancestral gene duplication events as well as identifying genes that have diverged from a common ancestor under positive selection. There are various tools available, such as MSOAR, OrthoMCL and HomoloGene, to identify gene families and visualise syntenic information between species, providing an overview of syntenic regions evolution at the family level. Unfortunately, none of them provide information about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. The Ensembl GeneTrees computational pipeline generates gene trees based on coding sequences and provides details about exon conservation, and is used in the Ensembl Compara project to discover gene families.基因重复（Gene duplication）是催生进化创新的关键因素，基因家族的收缩或扩张往往与物种的形态、生理及环境适应性紧密关联。对同源基因（homologous genes）的研究有助于解析基因家族的演化规律，这对于追溯祖先基因重复事件，以及鉴定在正选择（positive selection）作用下由共同祖先分化而来的基因均具有重要价值。目前已有多款工具可用于鉴定基因家族并可视化物种间的共线性信息（syntenic information），例如MSOAR、OrthoMCL与HomoloGene，这类工具能够从家族层面概述共线性区域的演化概况。但遗憾的是，上述工具均无法提供基因内部的结构变异相关信息，例如多基因组间祖先外显子边界（exon boundaries）的保守性特征。Ensembl GeneTrees计算流程（Ensembl GeneTrees computational pipeline）可基于编码序列（coding sequences）构建基因树，并提供外显子保守性的详细细节，该流程已应用于Ensembl Compara项目（Ensembl Compara project）以开展基因家族的发掘工作。