Retrogenomic software and databases to solve evolutionary questions

近二十年来，逆行元素的活动痕迹一直被用来研究不同脊椎动物分支之间和内部的系统发育关系。在哺乳动物中，许多系统发育问题已经通过插入逆转录病毒粒子作为系统发育标记得到了解决。然而，世界上只有少数几个实验室成功并有效地应用逆转录元素来研究进化。最有问题的任务是筛选基因组数据，以便从插入到保守基因组座位的数十万反转录病毒中挑选出能够提供可靠系统发育结果的少数几个。对不同逆转录元件性质的深刻了解和高通量生物信息学支持对这些研究至关重要；然而，支持这一领域研究的生物信息学工具很少。在过去的十年里，我们团队积累了大量的经验，并开发了许多利用逆转录元素作为系统发育标记的策略。我们开发了几种计算的、高通量的策略，并将这些策略应用于系统后基因组重建。我们现在已经开始将我们的知识转化为有用的、基于网络的生物信息学应用程序。科学家们要求使用TINT和GPAC工具来选择提取逆转录酶元件作为潜在的系统发育信息标记，这些工具已经在网上提供，但需要更全面、更综合的方法。我们打算推出一个模块化的生物信息学框架，用于基于逆转录酶标记规划系统后基因组项目，并分析在实验和电子研究中获得的逆转录元件的存在/缺失模式。我们计划向科学界免费提供这些工具，并将它们整合到世界范围内活跃的基因组测序项目的框架中。新的工具和数据库将在当地计算机服务器上维护，并不断开发和更新。

For nearly two decades, traces of the activities of retroposed elements have been used for examining the phylogenetic relationships among and within different clades of vertebrates. In mammals, many phylogenetic questions have already been resolved using insertions of retroposons as phylogenetic markers. However, only a few laboratories in the world have successfully and efficiently applied retroelements to investigate evolution. The most problematic task is screening genomic data to select from hundreds of thousands of retroposons inserted in conserved genomic loci the few that can provide reliable phylogenetic results. Profound knowledge of the nature of different retroelements and high-throughput bioinformatic support are essential for these studies; however, very few bioinformatics tools are available to support this area of research. During the last decade, our group collected a great deal of experience and developed many strategies for using retroelements as phylogenetic markers. We developed several computational, highthroughput strategies and applied those to retrophylogenomic reconstructions. We have now started to convert our knowledge into useful, web-based bioinformatic applications. The TinT and GPAC tools, requested by scientists for selecting extracting retroposon elements as potential phylogenetically informative markers, are already available on-line, but a more thorough, integrated approach is needed. We intend to derive a modular, bioinformatic framework for planning retrophylogenomic projects based on retroposon markers and for analyzing the presence/absence patterns of retroelements obtained in experimental and in silico research. We plan to make these tools freely available for the scientific community and to integrate them into the frameworks of world-wide active genomesequencing projects. The new tools and databases will be maintained on local computer servers and continuously developed and up-dated.