SI2-SSE: Software Infrastructure for Revealing Gene and Genome Evolution, Anchored by Enhancement of Multiple Genome Alignment Software MCSCAN

用于比对多个基因组的软件MCSCAN将得到增强，以有助于破译真核生物基因组和基因的结构和进化轨迹，特别是解决递归全基因组复制的后果。真核生物基因组序列的迅速发展为研究基因和基因组复制的功能和进化后果提供了新的基础，也为阐明特定基因之间关系的知识提供了手段。目前的软件只能对齐少量的基因组;并且由不同的基因组复制事件产生的复制块层不容易去卷积，因此无法提供理解基因组和基因家族进化轨迹的关键信息。增强的软件将减轻这些限制，大大帮助研究人员重建基因组和基因家族的进化轨迹，包括被子植物和其他经历过多倍化事件的类群的独特挑战性基因组。特别是，在（扩大数量的基因组的）多重比对之前，将在DNA水平上对同源区域进行多路比较，这将提供对不同复制事件产生的同源层的全息把握。为了反映结构变化的进化轨迹，基因组将以逐步的方式输入，首先是简单结构的基因组。由此产生的多重比对将更准确地描绘来自不同基因组的染色体区域之间的进化关系，并且容易被用户可视化和理解。该软件的核心部分将使用C++编程语言实现，而可视化模块将使用Python语言开发。多重和成对比对信息将存储在MySQL或SQLite数据库中。该软件将被驯服，以在多个操作系统下工作，包括MS Windows、UNIX和Linux。在线服务将使用Django Web框架和jQuery（一个简洁的JavaScript库）开发，并添加到我们支持NSF的PGDD中。该软件将由多个独立的模块组成，可供其他研究人员自由使用。与该软件配套的一个即将建成的网络服务器将显示基因组结构、不同植物之间的比较以及推断数百万年来发生的进化变化。这些直观的视觉资源将有利于寻求了解植物进化的研究人员，以及中小学学生和当地图书馆的读者。 该计划将定期接待来自其他机构，国家和公众的访客。增强的软件和基因组分析的相关结果将在学术会议上报告。

The software MCSCAN, used to align multiple genomes, will be enhanced to contribute to deciphering the structure and evolutionary trajectories of eukaryotic genomes and genes, in particular addressing consequences of recursive whole-genome duplications. Burgeoning sets of eukaryotic genome sequences provide the foundation for a new spectrum of investigations into the functional and evolutionary consequences of gene and genome duplication, as well as the means to clarify knowledge of relationships among particular genes. The current software can only align small numbers of genomes; and layers of duplicated blocks produced by different genome duplication events are not readily deconvoluted, thus failing to provide crucial information toward understanding evolutionary trajectories of genomes and gene families. The enhanced software will mitigate these limitations.The enhanced software will greatly help researchers to reconstruct the evolutionary trajectories of genomes and gene families, including the singularly challenging genomes of angiosperms and other taxa that have experienced polyploidization events. In particular, multiple alignment (of an expanded number of genomes) will be preceded by a multiple-way comparison of homologous regions at the DNA level, which will provide a holographic grasp of layers of homology produced by different duplication events. To reflect the evolutionary trajectories of structural changes, genomes will be input in a stepwise manner, with those of simple structures first. The resulting multiple alignment will much more accurately depict evolutionary relationships between chromosomal regions from diverse genomes, and easily be visualized and understood by users. The core part of the software will be implemented using the C++ programming language while the visualization module will be developed in Python language. The multiple and pairwise alignment information will be stored in MySQL or SQLite databases. The software will be tamed to work under multiple operating systems, including MS Windows, UNIX and Linux. Online service will be developed using the Django Web framework and jQuery (a concise JavaScript Library), and added to our NSF-supported PGDD. The software will be formed by several independent modules, which can be freely used by other researchers. A to-be-constructed web server accompanying the software will show figures illustrating genome structures, comparison between different plants, and evolutionary changes inferred to have occurred over millions of years. These intuitive visual resources will benefit researchers seeking to understand the evolution of plants, as well as elementary and middle school students, and readers at local libraries. The program will regularly host visitors from other institutions, countries, and the public. The enhanced software and related results in genomic analysis will be reported in academic conferences.